Systems and methods for genomic and genetic analysis

ABSTRACT

The present invention relates to a method for genomic and/or genetic analysis of a human nucleic acid sample, the method comprising the steps of providing a group of human reference genomes; testing of the human nucleic acid sample for sex and/or ancestry; selecting one or more population-specific human reference genomes, PHREGs, from the group of human reference genomes on the basis on the results of the sex and/or ancestry test; and aligning the human nucleic acid sample to the selected PHREGs; and variant calling against the selected PHREGs. The present invention also provides respective computer systems and computer programs.

The present invention relates to systems and methods for genomic and genetic analysis of a human nucleic acid sample.

BACKGROUND OF THE INVENTION Next-Generation Sequencing (NGS)

Next-generation sequencing, also known as high-throughput sequencing, is a routine method for the high-throughput and parallel sequencing of nucleic acid fragments which is well known to the person skilled in the art. The equipment and methodology of next-generation sequencing is commercially available from diverse suppliers (see, e.g., www.illumina.com).

Next-generation sequencing is the catch-all term used to describe a number of different modern sequencing technologies including:

-   -   Illumina (Solexa) sequencing     -   Ion torrent: Proton/PGM sequencing     -   SOLiD sequencing.

NGS technologies produce high-quality DNA sequences (“reads”). These reads are substantially shorter than the reads produced by the capillary-based Sanger sequencing technology (650-1000 bp), developed by Frederick Sanger and colleagues in 1977, which was the most widely used sequencing method for approximately 30 years. Sanger reads are produced in low-throughput with high costs, while the NGS methods produce much shorter reads (25-500 bases) at moderate costs. However, the total number of base pairs sequenced in a NGS run is orders of magnitude higher. These two factors cause many new informatics challenges, including the ability to process these millions or even billions of short NGS reads. The reads are usually processed in one of two ways: either they are mapped back to their correct locations in an existing backbone/reference sequence, building a sequence that is similar but not necessarily identical to the backbone sequence (called “read mapping”), or they are built into a new sequence (called “de novo assembly”).

The primary advantage of read mapping back to a reference genome as opposed to de-novo assembly is that it greatly simplifies the process of genome inference. While assembly needs to discover the entire genomic sequence and gives rise to many ambiguities, reference-based resequencing only needs to discover a sample's differences from the reference. In terms of complexity and time requirements, de novo assemblies are orders of magnitude slower and more memory intensive than mapping assemblies.

Read mapping is the first and most fundamental step in NGS analysis pipelines that aim to discover the variation of a newly sequenced human genome (or fractions of it, like the exome or a small targeted panel of genes) with respect to the previously sequenced human reference genome.

Read mapping is also used to align these millions or billions of short NGS reads to detect the coverage (the number of reads at a particular position/locus) which is a key quality parameter of the NGS experiment and all further derived conclusions.

The Human Reference Genome (HRG)

In February 2001 the Human Genome Project, a U.S. federal government effort, together with Celera Genomics, a private company, successfully completed drafts of the entire human genome, which was revised several times subsequently ^([Lander et al. 2001, Venter et al. 2001, Church et al. 2011]). Over a number of years, the genome assembly has steadily improved and new versions (“builds”) have been released, to the point that the current Genome Reference Consortium (GRC) human genome assembly, GRCh38 ^([Schneider et al. 2017]), is arguably the best assembled mammalian genome in existence, with just 875 remaining assembly gaps and fewer than 160 million unspecified “N” nucleotides (as of GRCh38.p8), whereas the first version had ˜150,000 gaps ^([Editorial (October 2010). “E pluribus unum”. Nature Methods. 7 (5): 331. doi:10.1038/nmeth0510-331]).

The HRG is the single most important resource used in human genetics and genomics today. It acts as a universal coordinate system and as such is the space in which annotations (genes, promoters, etc.) and genetic variants are described^([Harrow et al. 2012; ENCODE, 2012; 1000 Genomes Project Consortium, 2012]). It is also the reference for the read alignment step in next-generation sequencing analysis pipelines. Downstream of this mapping, it is used for functional assays and variant calling pipelines ^([Li H & Durbin 2009; DePristo et al., 2011]).

The initial build of the HRG was composed of DNA sequences from a small cohort of thirteen anonymous DNA donors who had volunteered in Buffalo, N.Y. with primarily European origins ^([Snyder et al]). Donors were recruited by advertisement in the Buffalo News, on Sunday, Mar. 23, 1997. The first ten male and ten female volunteers were invited to make an appointment with the project's genetic counselors and donated blood from which DNA was extracted. As a result of how the DNA samples were processed, about 80 percent of the reference genome came from eight people. One male, designated as RP11, accounted for 66 percent of the total.

To identify and resolve larger assembly issues, e.g. complex regions containing large-scale duplications and structural variations, sequence data from new genome mapping technologies and single haplotype resources originating from new donors have been brought into the most recent builds. At the time of filing the present application, GRCh38 contains sequences from about 50 different individuals, see http://www.bio-itworld.com/2013/4/22/church-on-reference-genomes-past-present-future.html.

Limitations of the HRG

1. The HRG is Linear

The human DNA is packaged into physically separate units called chromosomes. Humans are diploid organisms, containing two sets of genetic information, one set inherited from the mother and one from the father. Thus, each somatic cell has 22 pairs of chromosomes called autosomes (one member of each pair from each parent) and two sex chromosomes (an X and a Y chromosome in males and two X chromosomes in females). Each chromosome contains a single very long, linear DNA molecule. In the smallest human chromosomes, this DNA molecule is composed of about 50 million nucleotide pairs; the largest chromosomes contain about 250 million nucleotide pairs.

The diploid human genome is thus composed of 46 single DNA molecules of 24 distinct types. Because human chromosomes exist in pairs that are almost identical, only 3 billion nucleotide pairs (the haploid genome) needed to be sequenced to gain complete information concerning a representative human genome. The human genome is thus said to contain 3 billion nucleotide pairs, even though most human cells contain 6 billion nucleotide pairs. The haploid human genome consists of 22 autosomal chromosomes and the Y and the X chromosomes.

Each of the chromosomes represents a single DNA molecule, a sequence of millions of nucleotide bases. These molecules are linear, so one might expect that each chromosome should be represented by a single, continuous/linear nucleic acid sequence. Unfortunately, this is not the case for two main reasons: 1) because of the nature of genomic DNA and the limitations of sequencing methods, some parts of the genome remain unsequenced, and 2) some regions of the genome vary so much between individual people that they cannot be represented as a single continuous sequence. However, the HRG is represented as 24 linear DNA sequences consisting of the normal bases (A, C, T or G) with gaps represented as a series of “N”s clearly showing the position of gaps in the assembly.

The primary goal of the Human Genome Project was to produce a single representative sequence albeit with regions of uncertainty—that is, a single “scaffold”—for each physical chromosome. It also included a handful of alternate scaffolds representing allelic variation (different versions of the DNA bases present at a SNP locus are referred to as alleles), but they had no formalized relationship to the main scaffold. Recognizing that some highly polymorphic regions of the genome were particularly poorly represented by a single reference sequence, a formal model to introduce representative alternate versions of highly variable regions was added starting with GRCh37 ^([Church et al. 2011]). Sequences in the form of kilobase to multi-megabase “alternate locus scaffolds” were described relative to the “primary” (haploid) assembly, anchored to locations along the primary scaffolds. In the assembly at the time of filing the present application (GRCh38.p9), these cover 178 regions and total 261 linear sequences ^([Paten et al. 2017]).

Another complicating factor is that the HRG was deduced in the original international genome sequencing project from a collection of DNAs from multiple anonymous individuals. Thus, the resulting HRG is really a randomly mixed conglomerate, a haploid mosaic of different DNA sequences, that, in some cases, may be impossible to represent correctly as a single linear sequence.

2. The HRG is Certainly not Disease Free

Chen & Butte (2011) identified 3,556 disease-susceptible variants including 15 rare variants (Major Allele Frequency <1%) in the HRG. Using a curated, high-quality quantitative human disease-SNP association database, the authors assessed the likelihood ratio of increased risk over healthy population on 104 diseases for the reference genome and found high risk for type 1 diabetes, hypertension and other disorders. This provides clear evidence that the HRG does not represent a regular person and is certainly not disease free. Although it has dramatically accelerated the analysis of personal genome sequencing efforts, focusing on variants different from the reference genome will likely miss many disease causal variants including rare variants ^([Chen & Butte 2011]).

3. Reference Allele Bias Towards European Ancestry

A major challenge in using the HRG assemblies in prior art NGS analysis pipelines is the fact that they are derived from DNA samples from a relatively small number of anonymous donors with a bias towards European ancestry and therefore represent a small sampling of the broad array of human genetic variation.

Despite the relative effectiveness and ubiquity of the reference as a coordinate system for the majority of the genome, there is increasing concern that using the HRG as a lens to study all other human genomes excludes a great deal of common human variation and introduces a pervasive reference allele bias ^([Petrovski et al. 2016, Paten et al. 2017]). Reference allele bias is the tendency to over-report alleles present in the reference genome and under-report other alleles whose underlying DNA does not match a reference allele ^([Degner et al. 2009, Brandt et al. 2015]).

This bias arises chiefly during the read mapping and alignment step in resequencing experiments. To map correctly, reads must derive from genomic sequence that is both represented in the reference and similar enough to the reference sequence to be identified as the same genomic element. When these conditions are not met, mapping errors introduce a systematic blindness to the true sequence ^([Paten et al. 2017]). Reference allele bias also has the potential to affect some genetic subpopulations and some regions of the genome more than others, depending on the ancestral history of the reference genome at each locus bias ^([Petrovski et al. 2016, Paten et al. 2017]). Highly polymorphic regions such as HLA genes are especially susceptible to the effects of reference allele bias ^([Nielsen et al. 2011]), particularly when a single reference genome is used as an index for the alignment of NGS reads. In this situation, many true variants fail to be identified because they are present in haplotypes that differ from the genome used as index, and thus reads generated from these regions are not aligned and are lost ^([Brandt et al. 2015]).

As described above, reference bias is a known issue in human genome resequencing using the HRG for variant detection, and modifications to the reference can improve calling accuracy and interpretability ^([Fakhro et al. 2016]). One approach to mitigate this issue is to modify variant prevalence information early on in the genome-interpretation process by modifying the reference genome, such that variants discovered in the genome are the minor allele in the population ^([Dewey et al., 2011]). This modification to the reference results in a streamlined analysis workflow, as the number of false positives can be reduced and fewer variants need to be interpreted ^([Fakhro et al. 2016]).

The Future: Graph-Based Reference Structures/Genome Graphs

There is increasing recognition that a single, haploid reference genome is a poor universal reference structure for human genetics and genomics, because it represents only a tiny fraction of human variation: there exist variants and annotations that can not easily be described with respect to the reference genome ^([Horton et al. 2008, Pei et al. 2012]). Furthermore, as a target for read mapping and interpretation, it introduces a reference allele bias as described above. To mitigate these issues, recent versions of the reference genome assembly, such as the human genome assembly at the time of filing the present application (GRCh38.p9), have included “alternate locus” sequences (“alts”): additional multiple sequence representations of regions of the human genome considered to be highly polymorphic, anchored at their ends to locations within the “primary” (haploid) reference assembly. Such a structure, which contains multiple partially-overlapping sequence paths, can be considered a form of a mathematical graph: a genome graph ^([Novak et al. 2017]).

Graphs have a longstanding place in biological sequence analysis, in which they have often been used to compactly represent an ensemble of possible sequences. As a rule, the sequences themselves are implicitly encoded as walks in the graph. This makes graphs a natural fit for representing reference cohorts, which are by their nature ensembles of related sequences ^([Paten et al. 2017]). The graph contains not only the sample's approximate sequence, but also many of its specific variants.

Genome graphs are expected to produce improvements in read mapping, variant calling, and haplotype determination. It is anticipated that graph-based references will supplant linear references in humans and in other applications where cohorts of sequenced individuals are available ^([Novak et al. 2017]). Various projects are underway to build and apply these genome graphs. Genome graphs can now be built from libraries of common variants, and some tools, though still experimental, illustrate the huge potential of the graph-based approach.

Despite the theoretical advantages, research on variant calling using genome graphs is still relatively nascent. There is a number of questions yet to be tackled. How should duplications and repeats be represented? How can one best map to a graph? How should short variants whose homologies are unclear be parsed? How can graphs be used to enable a more comprehensive taxonomy of variation? These questions all represent open avenues for future research.

To be useful in practice, genome graphs must be able to translate their promised reduction in reference bias into measurable improvements in variant calling over established methodologies. Accordingly, developing variant calling algorithms for genome graphs is currently an important research frontier.

The Qatar Genome (QTRG)

Qatar is a small peninsula on the Persian Gulf with a total population of approximately 300,000 Qatari citizens. Qataris have one of the highest rates of consanguineous marriages in the world, which is still increasing, and the rate of endogamous marriage in Qatar approaches ˜100%. All these factors together with the large family size are the main reasons for the high rate of indigenous genetic diseases, which represent a financial burden on the Qatari budget. These factors triggered the Qatari government to seek a means to protect their own people from the threat of genetic diseases ^([Zayed 2016]).

Government officials decided to launch the Qatar genome project (QGP) in 2013 (http://www.gulf-times.com/story/374345/Qatarlaunches-genome-project). The intent of the project was to sequence the genome of each Qatari citizen in an effort to protect Qataris from the high rate of indigenous genetic diseases by allowing the mapping of disease-causing variants/rare variants and establishing a Qatari reference genome as a path towards personalized medicine. The final goal of the project is to apply the information to clinical practice and to allow this approach to become a routine part of the Qatari healthcare system ^([Zayed 2016]). To achieve the expected clinical application promise of the QGP, several serious challenges must be met, including reaching high variant-calling sensitivity and accuracy ^([Kobodt 2010]).

To facilitate precision medicine in regions of the Middle East and North Africa, a population-specific genome, custom tailored to disease research in the indigenous Arab population of Qatar (QTRG) was constructed by incorporating allele frequency data from whole genome sequencing of 1,161 Qataris, representing 0.4% of the population. A total of 20.9 million single-nucleotide polymorphisms (SNPs) and 3.1 million inDels (insertions and deletions) were observed in Qatar, including an average of 1.79% novel variants per individual genome ^([Fakhr et al. 2016]).

1000 Genomes Project (1 kG)

The 1000 Genomes Project was formed in 2008 to sequence and generate a catalog of human genetic variation (with respect to HRG GRCh37) and haplotypes from the genomes of at least 1,000 people around the world (hence the name the 1000 Genomes Project). The current phase 3 analysis of the project contains 2,504 individuals from 26 populations and defined 5 so-called super-populations, which are formed as unions of 4 to 7 populations each ^([1000 Genomes Project Consortium et al. 2015]). This haplotype resource at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels ^([Baye, 2011]).

Objectives of the Invention

Recent advances in NGS technologies allow for quick and cheap DNA and RNA sequencing, and as such have revolutionized the study of genomics and molecular biology. Genome sequencing projects for healthy and disease cohorts have identified numerous functional or disease-associated genomic variants, which can give clues about therapeutic targets or genomic markers for novel clinical applications.

Genetic variant calling is predominantly based on alignment of raw sequence reads against a reference genome (read mapping). This alignment-based approach has many limitations including incompleteness of genome assembly ^([Meyer, L. R. et al., 2013]), structural variations existing in the genomes of normal individuals ^([Sudmant et al., 2015]), sequencing errors in reads, and interference of single-nucleotide polymorphisms (SNP) on read mapping ^([Iqbal, Z. et al., 2012]).

Currently, at the time of filing the present application, read mapping against the linear HRG is the standard approach and is expected to remain the standard in clinical NGS analysis pipelines and resequencing human individuals, due to the relative effectiveness and ubiquity of the HRG as a coordinate system for the majority of the genome. In addition (and in contrast to the nascent state of genome inference using genome graphs), many successful methodologies have been published for calling variants using the linear reference genome ^([Nielsen et al. 2011]).

However, as described above, one major issue is bias in the HRG, ignoring prior information about genetic variation within the species. At present, the issue is typically solved by modifying the reference genome, such that variants called against the modified reference genome are the minor allele in the population.

The success of clinical genomics using NGS technologies requires the accurate and consistent identification of personal genome variants. A prerequisite for these objectives is accurate read mapping (alignment) and later variant calling.

One objective of the invention is the detection of new biomarkers, in particular genetic variants such as single-nucleotide variants (SNVs), insertions and deletions (inDels), copy number variations (CNV) and structural variants (SVs), e.g. chromosomal translocation, inversion, duplication, large inDels, for the usage of next-generation sequencing in human genome research.

Another objective is to increase the accuracy and confidence of the existing NGS based biomarkers e.g. as used for cancer treatment where the technique is used for analyzing the tumor cells and their damaged DNA.

DISCLOSURE OF THE INVENTION

In accordance with a first aspect of the invention, the present invention provides a method for genomic and/or genetic analysis of a human nucleic acid sample comprising the following steps:

-   a) providing a group of human reference genomes; -   b) testing of the human nucleic acid sample for sex and/or ancestry; -   c) selecting one or more population-specific human reference genomes     (PHREGs) from the group of human reference genomes on the basis of     the results of the sex and/or ancestry test in step b); and -   d) aligning the human nucleic acid sample to the PHREGs selected in     step c).

“Population-specific human reference genomes” (PHREGs) are understood in the following as ancestry-specific reference genomes and sex-specific reference genomes. PHREGs minimize the reference bias considerably and improve the alignment accuracy, and, if variant calling is performed subsequently, the variant calling accuracy. Advantageously, the invention does not only improve the precision of the alignment, but also improves calculation speed, the number of correctly aligned reads and the number of calculation steps of the alignment. The benefit of using PHREGs in the genomic and/or genetic analysis of a human nucleic acid sample can also result in an improved read coverage depth and can be assessed by an improved variant calling sensitivity.

In the context of the present invention, the term “human nucleic acid sample” generally means any nucleic acid sample which is isolated from a human sample. The human nucleic acid sample may in particular include NGS reads as defined in more detail below.

The human nucleic acid sample may generally comprise samples from all kind of standard biochemical, molecular and/or cell biological procedures which are suitable for the preparation of human nucleic acid. Such procedures comprise paracentesis, biopsy, liquid biopsy, cell free DNA isolation kits, or the like. The human nucleic acid sample may be or be derived from all kinds of suitable sources, including, but not limited to, body fluids, mucosa, tissues, tissue extracts or cells or any combination thereof. The human nucleic acid sample may also be a control sample derived from all kinds of suitable sources. The human nucleic acid sample may e.g. comprise blood samples, blood plasma samples, urine samples, tumor samples, possibly including undesired artefacts caused by the fixation in the tissue handling procedure FFPE (formalin-fixed paraffin-embedded tissue or formaldehyde-fixed paraffin-embedded tissue).

The human nucleic acid sample may in particular comprise DNA, RNA and/or size fractionated total DNA or RNA. Providing DNA from a sample of interest may include one or more biochemical purification steps such as, e.g., centrifugation, lysis and/or fractionation steps, cell lysis by means of mechanical or chemical disruption steps including, but not limited to, multiple freezing and/or thawing cycles, salt treatment(s), phenol-chloroform extraction, sodium dodecyl sulfate (SDS) treatment and proteinase K digestion. Optionally, providing DNA from a sample of interest may further include the removal of large RNA, such as abundant ribosomal rRNA, by precipitating in the presence of polyethylene or salt, or the removal of interfering sodium dodecyl sulfate (SDS) by precipitation in the presence of salt, preferably in the presence of potassium chloride solution. Methods of purifying total DNA or RNA from a cell and/or a tissue are well known to a person skilled in the art and include, e.g., standard procedures such as the use of guanidinium thiocyanate—acidic phenol-chloroform extraction (e.g. TRIzol®, Invitrogen, USA). Equally preferred, however, is that DNA from the sample of interest is provided without any of the herein described biochemical precipitation and/or purification steps.

In the context of the present invention, the term “nucleic acid” generally refers to any kind of single stranded or double stranded oligonucleotide molecule composed of either deoxyribonucleotides or ribonucleotides or both, including genomic DNA, nuclear DNA, somatic DNA, germline DNA, synthetically designed and/or manufactured DNA, including, but not limited to, in vitro generated DNA derived from messenger RNA profiles, preferably in form of cDNA. The term “nucleic acid” generally means single stranded or double stranded oligonucleotide molecules of identical or similar length, i.e. composed of either an identical or similar number of nucleotides.

The human nucleic acid sample may comprise genomic sequences which may serve for evaluating, analyzing, aligning, indexing and/or profiling of specific mutations on genomic, transcriptional or post-transcriptional level. As such, a human nucleic acid sample according to the present invention may refer and include, but not be limited to, any kind of coding regions, non coding regions, exons, introns, chromosomal and/or intra chromosomal regions, promoter regions, enhancer regions, regions encoding small and/or long regulatory RNAs, regions of active transcription and/or non transcribed regions, transposons, regions of hot spot mutations, regions of frame-shift mutations etc. and alike.

The “group of human reference genomes” comprises at least two human reference genomes, preferably a plurality of human reference genomes. The sex and/or ancestry test in step b) allows for the selection of one or more of the best suited human reference genomes from the group of human reference genomes in step c). In the preferred case, the sex and/or ancestry test in step b) leads to an auto-classification of the sex and/or ancestry and allows for the selection of one PHREG from the group of human reference genomes for the subsequent alignment step d), but the selection of one or more additional PHREGs for the subsequent analysis is also possible.

Preferably, the sex and/or ancestry test in step b) is based on an ancestry- and/or sex-specific subset of sequence variants related to sex and/or ancestry extracted from a curated database. Preferably, these sequence variants are single nucleotide polymorphisms (SNP)s and/or single nucleotide variants (SNV)s. The subset of sequence variants used for the sex and/or ancestry test is also referred to as Population dependent Human Ancestry and Sex Patterns (PHASPs). Preferably this curated database comprises all known sequence variants of all populations. The PHASP dataset is an excerpt of the curated database. It is a much smaller data set than the PHREG dataset and is the most discriminating set for the classification. Techniques used to generate PHASPs are computational methods from machine learning including feature reduction where features are genotypes. These learnings may be compared and tested with standard classification results.

Preferably, the sex and/or ancestry test includes a preliminary alignment step to detect the individual sequence variation pattern of the sample, wherein the human nucleic acid sample is aligned to a single human reference genome, for example GRCh37 or GRCh38. This single human reference genome used for the test in step b) is not ancestry or sex specific. By comparing the sequence variant pattern of the sample with the PHASP dataset, the patient's ancestry and sex is determined.

According to one embodiment, the testing may comprise a sex test. According to another embodiment, the testing may comprise an ancestry test. According to still another embodiment, the testing may comprise a sex test and an ancestry test.

In one exemplary embodiment, the group of human reference genomes comprises both male and female reference genomes. If the sex test in step b) determines that the human nucleic acid sample is a male or a female reference genome, then in step c), the respective male or female reference genome or genomes will be selected as the respective PHREGs for the subsequent alignment step d).

As sex chromosomes contain homologous sequences, using a sex-adjusted reference genome (with chromosomes X and Y for males, and without chromosome Y for females) will prevent misalignment of reads. Therefore, using sex-specific reference genomes reduces subsequent false positive and false negative variant calls.

In another exemplary embodiment, the group of human reference genomes comprises a number of ancestry-specific reference genomes. The ancestry test in step b) determines the best one or ones out of the number of ancestry-specific reference genomes. Then in step c), the closest one or ones will be selected as the PHREG or PHREGs for the subsequent alignment step d).

Choosing an incorrect ancestry can lead to large amounts of false positive and false negative variant calls. Using ancestry-specific reference genomes effectively increases the number of correctly aligned reads and reduces the false positives and false negatives.

Likewise, a combination of a sex and ancestry test is decisive in case that the group of human reference genomes comprises ancestry-specific male reference genomes and ancestry-specific female reference genomes.

The term “testing” in step b) is to be understood as encompassing at least one genetic and/or genomic test of the human nucleic acid sample. Genetic and/or genomic testing is more reliable than any information derived from “self-reporting”. Self-reported and investigator-assigned ancestry typically relies on the subjective interpretation of a complex combination of both genetic and non-genetic information including behavior, cultural, and societal norms, skin color, and other influences. It is rarely the case that a study participant or patient will report his/her ethnicity without errors. Self-reported ethnicity errors may occur for various reasons; some people may not be fully aware of their true ancestry or only know recent ancestry (or their geographic origin) while others may identify with one ethnic group despite their admixed background ^([Mersha & Abebe 2015]). Literature confirms that self-declared ancestry and sex are often incorrect ^([Ainsworth, 2015; Mersha & Abebe, 2015]). In fact, Ainsworth even explains that 1 person in 100 is affected by a disorder of sex development, leading to a physical appearance that does not match the person's genome.

Advantageously, the method can be also used as an additional quality check to identify sample swaps based on sex and ancestry. Mismatches between self-declared and predicted sex and ancestry in sequencing runs can reveal e.g. specimen transposition and other lab processing errors.

The term “alignment” generally means a computational step wherein a sequenced sample is compared with and fitted to a reference sequence. To this end, one needs to find the corresponding part of that sequence for each read in the generated sequencing data. In other words, alignment or read mapping is the process of determining the most likely source within the genome sequence for the observed nucleic acid sequencing read. In typical embodiments, the reads will be NGS reads, but it shall be understood that reads from other sequencing technologies are also encompassed by the teaching of the present invention.

The aligned reads derived from the human nucleic acid sample may be displayed, stored, printed, sent via a communication network, or otherwise processed further. Further applications or uses of the aligned human nucleic acid sample may in particular comprise one or more of the following:

1) Local realignment around insertions and deletions (inDels)

The term “inDels” means insertions or deletions of base pairs in the genome, typically including small genetic variations from 1 to 10000 bp in length. Realignment around inDels improves subsequent data analysis, in particular subsequent variant calls.

2) Base quality score recalibration (BQSR)

The term “base quality score” describes per-base estimates of error expressing how confident the base call made by the sequencing instrument is. The score may e.g. be used for weighing the evidence of subsequent variant calls. BQSR allows for adjusting the quality scores by taking into account systematic technical errors due to the physics or the chemistry of how the sequencing was performed.

3) Machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies

4) Variant discovery and genotyping to find all potential variants; herein also referred to as variant calling

Variant discovery may include the discovery of SNPs/SNVs, InDels, CNVs and SVs (chromosomal translocation, inversion, duplication, large inDels).

5) Evolutionary analysis studies

Evolutionary analysis studies may comprise tools measuring nucleotide diversity, population divergence, linkage disequilibrium, and the frequency spectrum of mutations from one or more populations. Evolutionary analysis may generally comprise computational tools for calculating evolutionary sequence statistics. The computational tools may be adapted to perform analyses in sliding windows across chromosomes or scaffolds. The computational tools may e.g. produce a phylogenetic tree of the sample.

Such evolutionary analysis may be performed e.g. by “POPBAM” software, described e.g. in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767577/.

6) Testing for wildtype biomarkers

Furthermore, the aligned human genome sample may be tested for the presence of wildtype biomarkers, i.e. biomarkers that will not be detected during variant calling because they are contained within the PHREG. The computation step after the alignment may thus comprise a test for each known biomarker, the test indicating whether the biomarker is present in the aligned human genome sample, irrespective of what the information of the PHREG at this position is.

According to one embodiment, the method comprises the additional step of performing variant calling of the aligned human nucleic acid sample with respect to the selected PHREGs. Advantageously, the invention improves the accuracy of variant calling by introducing the initial sex and/or ancestry test to determine the correct PHREGs for usage in the subsequent alignment and variant calling steps.

The aligned human nucleic acid sample, more specifically, the aligned NGS reads derived from the human nucleic acid sample may thus be further processed by one or more so-called variant callers which are computational modules, comprising different variant calling algorithms detecting any variant type (e.g. SNVs, InDels, Copy number alterations, structural variants). Subsequent method steps may comprise variant interpretation. The results of the variant calling and/or of the variant interpretation may be displayed, stored, printed, sent via a communication network, or otherwise processed further. Advantageously, the method will allow the detection of previously undiscovered biomarkers (e.g., in the context of cancer or other diseases) through the removal of bias from the used reference genome. In particular, the method according to the present invention allows for the discrimination of a variety of gene mutations, including, but not limited to SNVs, Multi-Nucleotide Variants (MNVs), complex events and large structural variants, in particular hot spot mutations, frame-shift mutations, non-silent mutations, stop-codon mutations, nucleotide insertions, nucleotide deletions, copy number variations, copy number alterations and/or splice sites.

The donor of the human nucleic acid sample can be a patient, i.e. a person having a disease or being suspected of having a disease. The application of the method, however, shall not be understood to be limited to patients only.

Variant calling and interpretation may comprise the analysis of genomic sequences indicative for the presence or absence of a certain disease. Based on the variant interpretation, the patient may be classified into a first group including patients where a certain treatment is not indicated, and into a second group including patients where a certain treatment is indicated. The invention may thus advantageously be used as a part of a disease screening procedure, evaluating the presence or absence of a disease in a patient.

Additionally or alternatively, the method may comprise a step of retrieving an indication of a disease related to, or associated with the human nucleic acid sample. The indication of a disease may be e.g. retrieved from an electronic health record or manually be entered via an input means of a computing device by the patient him/herself or by the attending physician. The indication may be identified according to disease ontologies, for instance ICD-10, MeSH, or MedDRA. For certain classes of indications there may also be specialized ontologies that may offer advantages like more precise categorization of the indication. In oncology it may be beneficial to use ICD-O-3 and/or the TNM staging system.

Based on the results of the variant calling and interpretation, and taking into account the disease of the patient, the method may involve providing a therapy plan for the patient. In the present context, the therapy plan may in particular be a personalized therapy plan for the patient, wherein the personalized therapy plan comprises treatment options tailored to the patient's genetic data, in particular to his/her clinical, molecular, and/or genetic condition.

In order to identify promising treatments for a patient, the method may comprise checking whether any of the variants, e.g. mutations found in the patient, e.g. in a patient's tumor or in the patient's normal control tissue, are indicative of the patient's outcome under any treatment. The method may further include identifying all treatments associated with any of the found variants. The method may include scoring the identified treatments and ranking the identified treatments according to the score to provide a treatment option or treatment contraindication prioritization for the patient.

In the context of the present invention, the term “treatment” includes the administration of a therapeutically effective drug or a pharmaceutically active compound in form of a pharmaceutical composition which prevents, ameliorates or treats the symptoms accompanying with the indication. The term “treatment” also includes any kind of surgery, radiotherapy and/or chemotherapy or any combination thereof.

For both alternatives, i.e. in the context of a screening method or a personalized therapy plan, the present invention may provide the physician with improved diagnostic capabilities, e.g. allowing for improved treatment decisions, because the precision of the alignment and the variant calling are improved.

According to one embodiment, the alignment is performed against the PHREG on a majority allele level. The majority allele level uses unique nucleotide codes (A,C,G,T) within the PHREG to adjust the reference sequence to a population. The single nucleotide is chosen which is most frequently observed at the given locus in the population. In case of ties in the allele frequency, the allele present in the underlying reference sequence (e.g. GRCh37 or GRCh38) may be used.

According to another embodiment, the alignment is performed against the PHREG on a non-rare alleles level. The non-rare alleles level uses ambiguity nucleotide codes according to the established IUPAC nomenclature ^([Cornish-Bowden, 1985]), e.g “R” for “A or G”. The non-rare alleles level may encode up to two or three, preferably two, alleles of substantial frequency in the population. Substantial frequency can be defined as being more than or equal to 30%, 20%, 15%, 10%, 5%, 3%, 1% or 0.1%, in particular more than or equal to 5%. As more than one variant allele per genomic position is incorporated into the PHREG, a more precise read alignment can be expected. In one embodiment, only single-nucleotide variations (SNVs) are considered in the non-rare alleles level. In other embodiments, inDels and other structural variations are considered as well.

According to one embodiment, the variant calling is performed against the PHREG on a majority allele level. In some embodiments, the alignment may be performed on a non-rare alleles level and the variant calling may be performed on a majority allele level. Alternatively, the variant calling is performed on a non-rare alleles level.

According to an embodiment, the human reference genomes provided in step a) are published human reference genomes. Published human reference genomes may in particular comprise the builds of the HRG, specifically the builds of GRCh37 and GRCh38. Additionally or alternatively, published human reference genomes may comprise the QTRG. Additionally or alternatively, published human reference genomes may comprise genomes derived from the 1000 Genomes (1 kG) project. For the 1 kG project, the VCF files for all chromosomes from the most current release on the 1 kG FTP site ftp[://]ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ may be downloaded and used. If more datasets with more individuals and ethnicities become publically available (e.g. the 1000 Arab genome project to study the Emirati population ^([Al-Ali, M. et al., 2018])), these could also be used in the method of the present invention.

Additionally or alternatively, the human reference genomes provided in step a) are derived from the published human reference genomes. The term “derived from” may in particular encompass error correction and/or adjusting the human reference genomes to a majority allele encoding level or to a non-rare alleles level.

Error correction may be performed such that reference nucleotides that are observed in zero individuals of a given population are replaced by the corresponding majority nucleotide.

In an embodiment, step a) comprises adjusting the human reference genomes to an encoding level, the encoding level comprising either unique nucleotide codes or ambiguous nucleotide codes. The encoding level comprising unique nucleotide codes may in particular be used to define the PHREGs on a majority allele level.

The encoding level comprising ambiguous nucleotide codes may in particular be used to define the PHREGs on a non-rare alleles level.

In one embodiment, for the adjustment to the encoding levels single-nucleotide variations are considered. For each population (or super-population) all reported SNVs together with their allele frequencies are used. In other embodiments, inDels, CNVs and/or SVs are also considered.

According to an embodiment, four different levels of adjusting the reference sequence to a population are proposed, wherein two of these are confined to unique nucleotide codes (A,C,G,T) and another two utilize ambiguous nucleotide encoding according to the IUPAC nomenclature ^([Cornish-Bowden, 1985]), e.g. “R” for “A or G”. These PHREG encoding levels are defined as follows:

1. Maximally conservative error correction: reference nucleotides that are observed in zero individuals of the population are replaced by the corresponding majority nucleotide, e.g. by the corresponding majority 1 kG nucleotide.

2. Majority allele: choose the single nucleotide which is most frequently observed at the given locus in the population (in case of ties in the allele frequency, the allele present in the underlying reference sequence, e.g. GRCh37 or GRCh38, is used).

3. Non-rare alleles: encode up to two alleles of substantial frequency (e.g. 5%) in the population, using IUPAC codes as necessary.

4. Complete modelling of observed alleles: encode at each position all (up to four) alleles that are reported in at least one individual of the population.

The complete representation of 1 kG variants in Level 4 PHREGs is, however, paid for by a disproportionately large number of genome modifications that introduce ambiguity and thereby may substantially impede the seed finding by read mappers. Therefore, in one embodiment, Level 3 is used for alignment using a IUPAC ambiguity-aware alignment algorithm. Since the currently best-performing variant callers are not designed to handle ambiguity codes, Level 2 PHREGs are used for subsequent variant calling unless better performing IUPAC ambiguity-aware alignment algorithms are available.

Advantageously, the method thus allows for user-defined levels of adjustments of the PHREG to population genetic variation, depending on the population(s) in focus and depending on the downstream analysis.

According to an embodiment, the human reference genomes provided in step a) are PHREGs. Step a) thus may comprise e.g. downloading the PHREGs from a public source.

As defined above, PHREGs are in a first place understood as ancestry-specific reference genomes and/or sex-specific reference genomes. In one embodiment, the human reference genomes provided in step a) are already population-specific because they comprise meta data indicating their ancestry and/or sex. For example, at the time of filing the present application, the current phase 3 analysis of the 1 kG project contains 2,504 individuals from 26 populations and from 5 so-called super-populations, which are formed as unions of 4 to 7 populations each. The 26 populations from the 1 kG study phase 3, and their associated 5 superpopulations (AFR, African; AMR, Ad Mixed American; EAS, East Asian; EUR, European; SAS, South Asian) can be found on http://www.internationalgenome.org/faq/which-populations-are-part-your-study.

In one embodiment, the data from the 1 kG project is used to build optimized population-specific human reference genomes for each of the 31 (super-) populations, and an additional super-population encompassing all other populations.

In case the human reference genomes provided in step a) are PHREGs, the public meta-data of the PHREG may as well be provided, e.g. via download from a public source. The meta-data may serve as a quality control for the method. If the meta-data and the sex- and ancestry classifier data coincide, then the quality control may be considered as successful. If not, the software may produce a warning or an alert which is displayed to the user, and, additionally or alternatively, the software may stop the procedure e.g. before the alignment step.

According to an embodiment, the sex test comprises at least one of the following: testing at least one position in a sex-specific gene on chromosome X and/or on chromosome Y; leveraging alignment differences of human genome samples on chromosome X and/or chromosome Y; cytogenetic tests; FISH analysis; CGH analysis, or any other experimental method allowing the determination of a human nucleic acid sample's sex, directly or indirectly.

The sex test may thus also be a result or a side product of a FISH analysis (fluorescence in situ hybridization analysis) ^([Gall J. G. 1969]) of the human nucleic acid sample. The sex test may thus also be a result or a side product of a CGH analysis (comparative genomic hybridization) ^([KallioniemiA. et al. 1992]) of the human nucleic acid sample.

The sex test enables efficient and reliable distinction of a male or female human nucleic acid sample.

As individuals from an ancestry or ethnicity share many SNPs that set them apart from other ancestries or ethnicities, the best-fitting PHREG for read alignment and variant calling can be identified by examining a range of ancestry-determining SNPs. The PHREGs may thus be selected from the group of human reference genomes on the basis of the results of an ancestry test.

Different experimental setups can be used in an upstream genomic analysis pipeline step to ascertain an individual's ancestry before proceeding with the alignment, to determine the best matching PHREG reference and to avoid errors.

1) The ancestry test may be based on a machine learning algorithm used on a human nucleic acid sample, or on another classification scheme that leverages ancestry-specific variants. The ancestry test method may in particular be based on machine learning that leverages the genotypes of exonic positions, e.g. more than 100, 500, 1000, 2000 or preferably more than 5000 exonic positions.

2) The determination of relevant genotypes can be based on NGS data or on an alternative experimental approach, for example a SNP array, as it is done in forensics research ^([Fondevila et al. 2013]) Here, the use of non-coding SNPs can help determining ethnicity.

3) The same non-coding SNPs (plus flanking regions) as tested in the forensic SNP array from alternative 2) could be added to existing targeted NGS panels to determine relevant genotypes.

In particular, the ancestry test may comprise using the genotype of at least one genomic position.

In one particular embodiment, the ancestry test comprises testing at least one gene selected from the enclosed sequence protocol. The 249 genes from the enclosed sequence protocol were shown to yield exact results.

Additionally or alternatively, the ancestry test may comprise the testing of SNP arrays and/or SNP chips and/or testing of markers from Sanger sequencing or mass spectroscopy, or any other experimental method designed to determine relevant genotypes.

In one particular embodiment, the ancestry test comprises testing at least one gene selected from the group of genes consisting of ABL2, ATP1A3, CIC, CYP2C8, CYP2C9, EPHA3, EPHA7, ERBB3, ERG, ETV1, F2, FAS, HFE, IL11RA, IL2RA, ITGB6, KIF11, KIT, KLK3, LRP6, MDM4, NAT2, NTRK2, PDGFB, PIK3R1, PLA2G3, PLAU, PRKCB, RICTOR, SLC7A11, STAT3, T, TSC1, VCAM1, VDR, VEGFB, ACVRL1, AXL, CA9, CALCR, CASP9, ENG, EPHB1, ERBB4, ESR1, FGFR2, HPSE, HSP90AA1, ITK, MRE11A, PLK1, PTPRC, SERPINE1, SMC4, TERT, TLR3, WISP3, WT1, XRCC1, ANGPT2, ARID2, BARD1, CBR3, CDH2, CYP1B1, DDR2, DNMT3A, EPCAM, ERCC2, FANCG, FANCL, GSTP1, IRS2, ITGB1, JAK3, LHCGR, MSH6, NCF2, RNF43, SLC5A5, TMPRSS2, TNFRSF8, AKT1, CD248, CD4, ESR2, EZH2, IGF1R, ITGAV, ITGB2, KLHL6, MAP3K1, MET, MLL, MTHFR, NFKB1, NUP93, PARP8, RB1, RPE65, TSHR, ABL1, BLM, CYP19A1, DPP4, EPHA6, ERBB2, EWSR1, FOXP4, ITGAM, KDM5A, LPA, LTK, MLH1, PBRM1, PHLPP2, SF3B1, TNFRSF10A, ABCG2, ACPP, ADAM15, DPYD, EPHA5, EPHB6, FOLH1, KDR, MSH3, MST1R, NTRK1, ROCK2, SLC6A2, TET2, TGM2, TH, ABCB1, CD22, CD40, CD44, CDH20, CYP11B2, ERCC5, GPR124, IL7R, ITGB3, ITGB5, NCL, NOD2, NR4A1, PGR, PLCG1, PPP2R1A, PRAME, PTCH2, RET, SETD2, XPC, ASXL1, EPHB4, PLA2G6, SYK, TET1, EP300, FLT1, ITGA1, LOXL2, PDGFRB, PIK3CD, SSTR5, TEC, APC, ATR, CLU, CREBBP, CYP2D6, EML4, MMP2, PARP2, PDGFRA, TRPM8, CSF1R, DOT1L, FGFR3, FGFR4, GLP2R, IKBKE, JAK1, NOTCH2, SPEN, SPG7, BRCA1, CYP11B1, GNAS, ITGA5, LTF, NRP2, PTK2B, TNKS, ABCC1, CEACAM5, CYP4B1, EGFR, FLT3, INSR, PTCH1, SMARCA4, ZNF217, BCR, EEF2, SELP, SLCO1B1, ABCC2, FLT4, MTR, IL4R, MTOR, RPTOR, TEK, ATM, CARD11, FANCD2, MEFV, NF1, TP73, BRCA2, CD109, PTPRD, ABCC6, IGF2R, P2RX7, ROS1, ACE, PARP1, PRKDC, CENPE, TSC2, ALK, NOTCH1, TNC, NOTCH3, POLE, MLL2, MYH11, POLD1, GRIN3B, F5, FANCA, LRP1B, LRP2, VWF.

In a more particular embodiment, the ancestry test comprises testing at least one of the genomic coordinates selected from the group of genomic coordinates listed in Appendix 1. Appendix 1 describes the GRCh37-based genomic coordinates of the features used for the ancestry classifier. The first 3 columns are formatted according to the BED file standard (https[://]www.ensembl.org/info/website/upload/bed.html) and (from the left to the right) correspond to chromosome, 0-based start of the feature, and 0-based end of the feature (i.e., the first position after the end of the feature). Column 4 shows the bases that are relevant to the classifier at this position, and column 5 the corresponding gene name.

Gene names were approved by the HUGO Gene Nomenclature Committee (HGNC, https://www.genenames.org/). HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication. The gene names used in the present application were retrieved in August 2013.

In another particular embodiment, the ancestry test comprises at least one of the SNPs listed in Appendix 2 ^([Fondevila et al. 2013]) Appendix 2 indicates the number of the chromosome on which an SNP is positioned (left column), the exact chromosomal position (middle column) as well as the corresponding rs number (right column). The rs number is an accession number assigned by the NCBI (National Center for Biotechnology Information) in its SNP database (dbSNP, https://www.ncbi.nlm.nih.gov/projects/SNP/) and it is widely used to refer to specific SNPs across genomic databases. When researchers identify a SNP, they send a report (which includes the sequence immediately surrounding the SNP) to the dbSNP database. If overlapping reports are sent in, they are merged into the same, non-redundant Reference SNP cluster, which is assigned a unique rsid. More information is available in the following url http[://]www.ncbi.nlm.nih.gov/sites/books/NBK44406/.

Such an ancestry test may comprise genetic and/or genomic tests enabling a distinction of ancestry categories. Such ancestry categories may be defined as AFR, AMR, EAS, EUR, SAS, in accordance with the 1 kG project. The method is, however, not limited to the 1 kG project data, e.g. in case that more comprehensive datasets with more individuals/ethnicities were/became available, these could be used for the same purpose alternatively.

According to an embodiment, the human nucleic acid sample comprises a set of reads issued from a next-generation sequencing procedure, and the alignment comprises a step of mapping the reads to the selected PHREGs. Additionally or alternatively, the human nucleic acid sample comprises a set of reads issued from a targeted sequencing procedure, e.g. from panel sequencing.

Advantageously, the method can be seamlessly integrated into any existing NGS analysis workflow which is based on read mapping against a HRG.

Aligning the human nucleic acid sample to the selected PHREGs by mapping the reads to the selected PHREGs may presuppose the preparation of sequencing libraries by random fragmentation of the DNA or cDNA sample, followed by 5′- and 3′-adapter ligation in advance. In some embodiments, the fragmentation and ligation reaction is combined into a single step, followed by PCR amplification of the adapter-ligated fragments.

Aligning the human nucleic acid sample to the selected PHREGs by mapping the reads to the selected PHREGs may presuppose the sequencing of this set of DNA fragments, resulting in reads of approximately between 28 base pairs (bp) and 1000 base pairs (bp) in lengths ^([Goodwin S. et al. 2016]). The set encompasses enough reads to reach a pre-determined target region coverage suitable for the experimental questions asked (typically between a few x and several 1000x).

In one embodiment, the next-generation sequencing procedure involves whole exome sequencing. In another embodiment, the next-generation sequencing procedure involves whole genome sequencing. The term “whole exome sequencing” generally means a technique for sequencing all the protein-coding genes in a genome (known as the exome). It consists of first selecting only the subset of DNA that encodes proteins (known as exons) and then sequencing this DNA using any high-throughput DNA sequencing technology. Humans have about 180,000 exons, constituting about 1.5% of the human genome, or approximately million base pairs. In particular, the exome sequencing may be carried out by next-generation sequencing. “Whole genome sequencing” (also known as WGS, full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria.

In accordance with another aspect of the invention, a computer system for gene analysis of a human genome sample comprises:

-   -   a) a first module comprising computer instructions for providing         a group of human reference genomes;     -   b) a second module for testing of a human nucleic acid sample         for sex and/or ancestry;     -   c) a third module comprising computer instructions for selecting         one or more population-specific human reference genomes, PHREGs,         from the group of human reference genomes on the basis of the         results of the sex and/or ancestry test; and     -   d) a fourth module comprising computer instructions for aligning         the human nucleic acid sample to the determined PHREGs

In particular, the computer system may be adapted for, or may be configured for performing any one of the methods disclosed above. Therefore, it is understood that features which have been described in the context of the methods are disclosed for the computer system, and, vice versa, that features which will be described in the context of the computer system are disclosed for the methods as well.

The modules may be software modules, software routines or software subroutines stored on a machine-readable storage medium such as a permanent or rewriteable storage means, or on a storage medium assigned to a computer means, for instance a mobile storage medium such as CD-ROM, DVD, Blu-ray disc, sticks or memory cards. Additionally or alternatively, the modules may be provided on a computer means such as a server or a cloud server for download, for example via a data network such as the internet or via a communication line such as a telephone line or a wireless line.

Any of the modules disclosed herein may be functional units which are not necessarily physically separated from each other. Several units of the modules may be realized in the form of one single physical unit, for instance if several functions are implemented in a software package.

The computer modules disclosed herein may not necessarily be part of an integral system, but may be distributed over several individual systems interacting with each other over a communication network.

According to one embodiment, the second module for testing of a human nucleic acid sample for sex and/or ancestry is a computer module comprising computer instructions. Additionally or alternatively, the second module may comprise a wet lab experiment, e.g. an experiment performing a FISH test. The results of the FISH test may be electronically or visually analyzed for determining the sex of the sample.

In accordance with yet another aspect of the invention, a computer program comprises instructions which, when the program is executed by a computer, cause the computer to carry out the steps a), b), c) and d) of any one of the methods described above.

In accordance with still another aspect of the invention, a computer-readable storage medium comprises instructions which, when executed by a computer, cause the computer to carry out the steps a), b), c) and d) of any one of the methods described above.

As already discussed above, the method of the present invention are especially suitable for identifying alterations in the genome of a patient which are indicative for a given disease or which are indicative for the susceptibility of the patient for a given treatment.

In this context, the term “disease” includes any disease which is characterized by one or more genomic alterations. This includes cancer, an autoimmune disease, a cardiovascular disease, and any inherited disease. The patient may be of any species but is preferably a mammal, more preferably a human.

Depending on the individual disease and treatment, the person skilled in the art will be able to select the individual treatment mode which is beneficial for the patient.

Consequently, in a further aspect of the invention, the invention relates to a method for diagnosing a disease in a patient comprising

retrieving an identification of a disease indication of the patient,

obtaining a nucleic acid sample from the patient, and

performing genomic and/or genetic analysis of the nucleic acid sample according to the method for genomic and/or genetic analysis of a human nucleic acid sample described herein, thereby determining the disease status of the patient.

The identification of a disease indication may be retrieved by any method known in the art, e.g. as a user's input, from an electronic health record or electronic medical record or from a patient database comprising medical records.

In the context of this aspect of the invention, the term “disease status” means in one embodiment that the disease of the patient is confirmed. In a further embodiment, this term means that the disease is diagnosed more accurately, i.e. that the individual subtype of the disease is determined.

The invention further relates to a method for treating a disease in a patient comprising

retrieving an identification of a disease indication of the patient,

obtaining a nucleic acid sample from the patient, and

performing genomic and/or genetic analysis of the nucleic acid sample according to the claimed method, thereby determining the disease status of the patient, and treating the patient.

In a further aspect of the invention, the invention relates to a method for determining whether a patient is susceptible to a treatment by a given drug comprising

retrieving an identification of a disease indication of the patient,

obtaining a nucleic acid sample from the patient,

performing genomic and/or genetic analysis of the nucleic acid sample according to the method for genomic and/or genetic analysis of a human nucleic acid sample described herein,

retrieving possible treatments for the disease indication of the patient,

performing variant calling and interpretation, and

classification of the retrieved possible treatments based on the variant interpretation, wherein a treatment is classified as indicated for the patient or contraindicated for the patient.

By this method, it is possible to determine which treatment is available or advantageous for the patient. For example, it is possible to determine whether the patient is susceptible to a given treatment or whether a given treatment is expected to have only acceptable side effects.

The identification of a disease indication may again be retrieved by any method known in the art, e.g. as a user's input, from an electronic health record or electronic medical record or from a patient database comprising medical records.

The possible treatments for the disease indication of the patient may be retrieved by any method known in the art, e.g. from a data base.

The invention also relates to a method of treating a patient comprising

retrieving an identification of a disease indication of the patient,

obtaining a nucleic acid sample from the patient,

performing genomic and/or genetic analysis of the nucleic acid sample according to the method for genomic and/or genetic analysis of a human nucleic acid sample described herein,

retrieving possible treatments for the disease indication of the patient,

performing variant calling and interpretation,

classification of the retrieved possible treatments based on the variant interpretation, wherein a treatment is classified as indicated for the patient or contraindicated for the patient,

selecting one of the indicated treatments, and

treating of the patient according to the selected treatment.

The identification of a disease indication may again be retrieved by any method known in the art, e.g. as a user's input, from an electronic health record or electronic medical record or from a patient database comprising medical records.

The possible treatments for the disease indication of the patient may again be retrieved by any method known in the art, eg from a data base.

BRIEF DESCRIPTION OF THE FIGURES

The foregoing and other objects, aspects, features, and advantages of the disclosure will become more apparent and better understood by referring to the following description taken in conjunction with the accompanying drawings, in which:

FIG. 1 is a flow diagram depicting a method for genomic and/or genetic analysis of a human nucleic acid sample in accordance with the present invention;

FIG. 2 is a flow diagram depicting methods for data analysis in accordance with the present invention;

FIG. 3 is a representation of read mapping steps;

FIG. 4 is a flow diagram depicting a method for genomic and/or genetic analysis of a human nucleic acid sample in accordance with the present invention;

FIG. 5 is a diagram representing the distribution of chosen features for the sex classifier by class computed on the MH Panel data; and

FIG. 6 are boxplots of memory usage and runtime of the two Ansextry classifiers (classifiers for sex and ancestry) and EthSEQ.

DETAILED DESCRIPTION OF THE FIGURES

FIG. 1 illustrates the general workflow for genomic and/or genetic analysis of a human nucleic acid sample, which comprises the process of extraction of the human nucleic acid sample, the preparation of a sequencing library, the sequencing and the subsequent data analysis. In the context of the present invention, the processes of extraction of the human nucleic acid sample, the preparation of a sequencing library and the sequencing may involve well-known standard processes and will not be explained in more detail. The inventive data analysis part is shown in FIG. 2 in more detail.

FIG. 2 shows the data analysis step of FIG. 1 comprising a first sex and ancestry test step, followed by an alignment (or read mapping) step, a variant calling step and an annotation step. The input file for the read mapping computational module is raw sequence data, e.g., in the form of a FASTQ file. The output file of the read mapping computational module is, e.g., a BAM file, being the input file for the variant calling computational module. The output file of the variant calling computational module is, e.g., a VCF file. The subsequent annotating computational module may annotate the data from the VCF file and export it in the required format, such as PDF, HTML, or the like. The file formats are merely exemplary and may be different, e.g. instead of BAM, there may be SAM or CRAM files, and the like. The data analysis pipeline in FIG. 2 may also comprise computer modules which transform the input or output files from one file format into another file format.

FIG. 2 also compares the prior art scenario with the scenario of the present invention. Prior art methods (referred to under “A” in FIG. 2) do not provide for a sex and ancestry test. Alignment and variant calling is thus performed against the standard HRG. The method according to the present invention (referred to under “B” in FIG. 2) provides a sex and ancestry test, which allows for the selection of one or more determined PHREGs. Subsequent alignment and variant calling is then performed against the determined PHREGs.

FIG. 3 is a schematic representation of an exemplary read mapping step. In the example, NGS reads carry an ancestry-specific SNP “A”. Ancestry-specific SNP “A” is located within the close vicinity of a previously undiscovered biomarker variant “G”. The vicinity can be up to the read length.

During alignment, the NGS reads will produce 2 mismatches when they are compared against the standard HRG, namely the ancestry-specific SNP and the biomarker variant. During alignment, the NGS reads will, however, produce only one mismatch, namely the biomarker variant, when they are compared against the corresponding PHREG, as the PHREG has been modified at the ancestry-specific position, such that the PHREG is identical to the ancestry-specific SNP.

The alignment algorithm uses a scoring system that involves penalties for every mismatch and/or gap between a sequenced read and the chosen reference genome. Reads are then aligned to the best-scoring position, or may not be aligned at all due to a low overall score, or too many genomic positions with equal alignment score. Because of mismatch penalties in the alignment algorithm, reads are less likely to be aligned against the HRG than against the PHREG, especially if further variants are within read length. The reads will thus be discarded or, in the worst case, even be aligned in a wrong position of the HRG.

Thus, PHREGs have the effect that reads originating from regions of ancestry-specific variation can be rescued, especially if they carry additional variants (e.g. disease causing variants) besides the ancestry-specific variation. This allows the detection of previously undiscovered biomarkers.

FIG. 4 shows a flow chart depicting a method for genomic and/or genetic analysis of a human nucleic acid sample according to the present invention.

In a first step, a group of human reference genomes is provided to a system comprising a processing unit. To this end, a first computer module of the system may download reference genomes from a remote facility, such as an internet database. The processing unit can be any programmable computer means which substantially includes at least a processor with an internal memory such as RAM (Random Access Memory), which allows for storing and executing instructions.

The processing unit has access to a non-volatile storage means in which data sets and computer files may be stored, e.g. human reference genomes, as well as clinical data and the genetic profiles of patients. The system has access to a communication network such as LAN or the internet.

In a second step, a computer module of the system adjusts the human reference genomes to an encoding level, preferably set by a user of the system. The encoding level may comprise unique nucleotide codes or ambiguous nucleotide codes. In some embodiments, four different levels of adjusting the human reference genomes to a population are proposed, wherein two of these are confined to unique nucleotide codes (A,C,G,T) and another two utilize ambiguous nucleotide encoding according to the IUPAC nomenclature, in particular maximally conservative error correction, majority allele level, non-rare alleles level and complete modelling of all observed alleles.

In a third step, a human nucleic acid sample of a patient is provided. To this end, another computer module of the system may download the raw sequence data, e.g. in the form of a FASTQ file, from a sequencing laboratory which performs the sequencing of a sample of interest on a remote platform. In an alternative embodiment, the sequencing is performed locally and the results are internally transferred. In the context of the third step, the system may also receive further clinical data of the patient from further input sources, e.g. the information about a disease the patient suffers from, information about current treatments, or the like. The clinical patient data may e.g. be directly received from the patient, e.g. may be typed on a keyboard or may be deduced from a free text typed on a keyboard, or may also be received from a multiple-choice element in a GUI. The clinical patient data may also be retrieved from an electronic health record (EHR) or from electronic medical record (EMR), possibly on a chip-card or in a database retrievable over a communication network.

In a fourth step, the human nucleic acid sample is tested for sex and/or ancestry. Again, the tests may be performed locally, or another computer module of the system may retrieve the results of the tests from an external service provider via a communication network. The sex and/or ancestry test may be performed by a second computation module or another wet lab experiment.

In a fifth step, one or more PHREGs are selected from the group of human reference genomes on the basis on the results of the sex and/or ancestry test in step. The selection may be performed by a third computation module.

In a sixth step, the human nucleic acid sample is aligned to the selected PHREGs. The alignment comprises mapping the set of reads issued from an NGS procedure to the selected PHREGs. The alignment may be performed by a fourth computation module, and the output file may be a BAM file.

In a seventh step, variant calling of the aligned human nucleic acid sample is performed with respect to the selected PHREGs. Before the variant calling takes place, a computer module of the system may re-adjust the human reference genomes to an encoding level, preferably set by a user of the system. The encoding level may comprise unique nucleotide codes or ambiguous nucleotide codes and be different from the encoding level used at the alignment step. Variants may be identified using best suited state-of-the-art algorithms. The variant calling may be performed by a fifth computation module, and the output may comprise sequence data in the form of variants with respect to the PHREG in variant call format (VCF file).

In an eighth step, variant interpretation is performed. The system may thus comprise a further post-processing computation module adapted for performing an analysis of the identified variants. In one embodiment, the post-processing module may analyze a set of genes and/or variants indicative for the presence or absence of a disease in the patient. Additionally or alternatively, the post-processing module may determine a set of treatments for the disease of the patient, taking the further clinical patient data into account, and may determine the best fitted personal treatment for the patient based on the patient's genetic data, in particular based on the identified genetic variants. In yet another embodiment, the post-processing module may perform statistics and determine mutational load, nucleotide substitution rates and hotspot mutations from the identified variations.

The variants found can also be used as an input for classifier predicting treatment efficacy or treatment safety or for classifier for diagnostic and/or therapeutic purposes.

In a ninth step, diagnostic and/or therapeutic implications may be generated and provided. To this end, the system may include an output interface in functional connection with any one of the third, fourth, fifth and the post-processing module, such that their results can be outputted. The output interface may be coupled to any display means or printers such that information calculated by the processing unit may be presented. Furthermore, there can be links to communication systems for an intranet and/or the internet such as a program for the sending and receiving of e-mails realized via an output interface.

FIG. 5 shows a diagram representing the distribution of chosen features for the sex classifier by class (F: female; M: male), computed on the MH Panel data. Colored vertical lines represent the class median. Top: chrX/chrY aligned read ratio; middle: for 500 common SNP positions on chrX, fraction of the major allele frequencies in bin 0.8-1.0; bottom: percentage of properly paired reads on chrY. FIG. 5 should be viewed in the context of the example described below.

FIG. 6 shows boxplots of memory usage (top, in GB) and runtime (bottom, in minutes) of the two Ansextry classifiers and EthSEQ on the 300 TCGA whole-exome samples. FIG. 6 should be viewed in the context of the example described below.

Example 1

AnSextry, a machine-learning based tool that derives sex and ancestry of a sample using read alignments from whole-exome sequencing data is presented. Self-declaration of both traits is known to be unreliable, and AnSextry predictions are useful both in the context of sample-swap detection and for unbiased genomic variant interpretation, especially in large cohort studies. A benchmark of AnSextry on over 1,300 samples showed high precision and low time and memory requirements.

1 INTRODUCTION

With the sharp drop in cost observed over the last decade, next-generation sequencing of large cohorts is becoming commonplace ^([Cancer Genome Atlas Research Network et al., 2013; Rand et al., 2016]), and whole-exome approaches play a major role in large studies, especially in the area of precision medicine or the comprehensive characterization of disease. In this context, reliable knowledge of a sample's ancestry and sex comes with multiple benefits. First, it can be used as an easy quality control to help identifying sample swaps arising from the complex protocols and manual work involved in sample processing. Second, ancestry is crucial for the interpretation of variant impact, to circumvent the strong European bias present in most genomic studies and in the human reference genome, and to improve clinical care for people with diverse ancestries ^([Petrovski et al., 2016; Mersha et al., 2015; Fakhro et al., 2016]). Finally, ancestry is widely used in genetic association studies to avoid false associations with disease due to population stratification ^([Wu et al., 2011]). Self-declaration of sex and ancestry is often unreliable ^([Mersha et al., 2015; Ainsworth, 2015]), calling for an identification using genomic information.

AnSextry, a machine-learning method based on logistic regression, was developed to quickly and reliably characterize sex and ancestry from whole-exome sequencing paired-end read alignments. The algorithm relies on standard file formats and can be readily integrated in an existing next-generation sequencing analysis workflow. It provides a ready-to-use model and only requires a simple BAM file as an input. In addition, its low memory requirements allow it to be run on a desktop computer. A benchmark against EthSEQ ^([Romanel et al., 2017]), the only other whole-exome, BAM-file-based ancestry inference tool known, shows that AnSextry compares favorably in terms of precision, runtime and memory usage. No other published method for sex prediction is known to date.

2 METHODS

2.1 Algorithm

A set of two classifiers was prepared, which infer the most probable sex and ancestry of an individual, based on whole-exome sequencing paired-end read alignments. This tool leveraged differences in read mapping and individual genotypes for its predictions.

The sex and the ancestry classifier were based on logistic regression using Python and the scikit-learn machine learning library. Features for both were derived from an input BAM file. Paired-end reads were aligned with BWA 0.7.15 with default settings for alignment and without post-processing steps like local realignment or duplicate removal. The GRCh37 reference genome was used without the non-chromosomal supercontigs and with masked pseudo-autosomal regions PAR1 and PAR2 to avoid alignment distortions on chromosomes X and Y. In the context of the present invention, the term “supercontigs” is generally to be understood as an ordered set of contigs, i.e. contiguous lengths of genomic sequence in which the order of bases is known to a high confidence level.

The sex classifier worked with two-class logistic regression using L1-regularization and returned a probability for each class. 5-fold cross-validation was used to determine a suitable regularization strength. The model yielding the highest area under the precision-recall curve for the training data was chosen as best model and evaluated on test data sets.

The ancestry classifier was based on multinomial logistic regression using L2-regularization and Principal Component Analysis, and returned a probability for each of the 5 continental ancestries defined in the 1000 Genomes Project: African (AFR), Ad Mixed American (AMR), East Asian (EAS), European (EUR), South Asian (SAS) (The 1000 Genomes Project Consortium et al., 2015). 5-fold cross-validation was used to determine suitable parameters. The model yielding the highest F1 score for the training data was chosen as best model and evaluated on test data sets.

2.2 Features

Features for the sex classifier were based on alignment differences between chromosome X and Y (FIG. 5). The chrX to chrY reads ratio as well as the percentage of properly paired reads on chrY were used. In addition, the major allele frequencies at 500 common exonic SNP positions on chrX were compounded. To avoid population bias, SNPs frequent across major ancestries were chosen.

For the ancestry classifier, the genotypes of all autosomal SNPs with a genomic position within the intersection of target regions of common Agilent All Exon kits (V5, V6, V6+COSMIC) and the Molecular Health Pan-Cancer gene panel (target size 2.9 Mbp) were determined from the 1000 Genomes data described in section 2.3. Feature selection was used to retain meaningful SNPs showing variance across ancestries, resulting in 10,000 genotypes corresponding to 5,040 genomic positions used as features for the classifier. A corresponding BED file can be found in Appendix 1 and could be used to determine overlap with any targeted sequencing kit.

2.3 Data

In order to obtain data from diverse ancestries, genotype data from 1735 individuals from the 1000 Genomes Project phase 3 was used to train and test the ancestry classifier. Continental ancestries (AFR, AMR, EAS, EUR, SAS) were used for classification and individuals were randomly chosen to achieve balanced classes. 694 individuals were part of the test set.

Primary whole-exome control data from 300 individuals with self-reported race and sex was downloaded from TCGA (cancergenome.nih.gov) as a test set, corresponding to 3 cancer types (urothelial bladder carcinoma, lung adenocarcinoma/squamous cell lung cancer, gastric adenocarcinoma). All samples were sequenced using the Agilent SureSelect Human All Exon 50 Mb kit. Records were chosen randomly to achieve balanced class sizes corresponding to TCGA categories: 150 male and 150 female individuals, as well as 100 white, 100 asian, and 100 black or African American individuals.

Targeted sequencing data from 988 cancer patients with self-reported sex, sequenced using the Molecular Health Pan-Cancer gene panel was used to train and test the sex classifier. Individuals were chosen randomly to achieve female/male class balance. 396 cases were randomly chosen as test data for the sex classifier. The 300 TCGA cases described above were used as an additional test set.

3 RESULTS

3.1 Sex classifier

The sex classifier was trained using 592 datasets sequenced with the Molecular Health Pan-Cancer gene panel. Paired-end reads were aligned and features computed as described in the Methods section. After tuning the method with cross-validation, performance was evaluated on two test datasets: 396 individuals sequenced with the abovementioned gene panel, and 300 TCGA individuals with whole-exome data available.

On the panel test data, the sex classifier reached an average precision of 97.5%, with 10 individuals (5 male, 5 female) being misclassified (see Table 1). Misclassification was not associated with lower coverage.

TABLE 1 Details on individuals sequenced with MH Panel where predicted sex did not match self-declared sex. Median coverage over all samples used was 2116x. The mean coverage of all misclassified samples was either close or above this median, showing that misprediction did not seem to be linked to lower-than-median coverage. Predicted probability for Mean coverage (with Sex Predicted sex true sex [%] duplicates) F M 39.0 2579 F M 15.3 2099 F M 33.8 1656 F M 17.1 1787 F M 0.8 1797 M F 0.0 6016 M F 28.0 2401 M F 0.3 3603 M F 0.0 1606 M F 0.0 1705

Since disorders of sex development are thought to occur with a frequency of 1% in the general population ^([Ainsworth, 2015]), it is possible that some of the misclassified cases were actually correctly classified, but had incorrect self-declared sex.

On the TCGA test data, the sex classifier reached a precision of 100%. All 300 individuals were correctly classified. In terms of runtime and memory usage, sex prediction took less than a minute in all cases with an average memory usage of 526 MB (FIG. 6).

3.2 Ancestry classifier

The ancestry classifier was trained on 1041 datasets from the 1000 Genomes Project. Individual genotypes were used as features, as described in 2.2. The best-performing model was evaluated on two test datasets: a remaining 694 individuals from the 1000 Genomes Project, as well as 300 TCGA individuals with sequenced whole-exomes.

The ancestry classifier reached a high average precision of 99% on the 1000 Genomes test data, performing best for Asian ancestries (100% precision both for South and East Asian), followed by African and South American ancestry (99% precision), and European ancestry (98%). In total, only 5 individuals out of 694 were misclassified.

On the 300 TCGA exome test datasets, the ancestry classifier reached a slightly lower precision of 96.33%, with a total of 11 individuals misclassified. These results were compared to EthSEQ ^([Romanel et al., 2017]), which is currently the only other ancestry prediction method known that provides a suitable pre-computed model and is designed to work out of the box on single whole-exome BAM files. Results were highly concordant between the two methods, however, the precision reached by EthSEQ was a bit lower (94%) with a total of 18 individuals misclassified. In addition, runtime and memory required by EthSEQ were much higher: while the ancestry classifier had an average runtime of 28 seconds with 540 MB average memory usage, EthSEQ, even with the use of multithreading (4 cores), took 4.8 minutes and 14.7 GB on average (FIG. 6).

As an important observation, the concordance between the two algorithms was also high for misclassified datasets: 10 out of 11 individuals whose ancestry prediction did not match the race provided by TCGA were also differently classified by EthSEQ, and in 8 out of 10 cases, both methods predicted the same ancestry. This suggests that at least a part of these individuals may have been wrongly categorized by TCGA, whose race information is based on self-declaration. 6 out of the 10 concordant cases were predicted as AFR or AMR, which is in accordance with Mersha et al. who claim that errors in self-declaration are most prevalent in African American and Latino populations. Table 2 shows misclassified individuals.

TABLE 2 Details on TCGA individuals where predicted ancestry (either by Ansextry, EthSEQ, or both) did not match TCGA self-declared race. TCGA race categories include “black or african american” (black/afr.am.), “white”, and “asian”. Unmarked rows corresponded to samples where neither Ansextry nor EthSEQ match TCGA race; rows marked with “*” were samples where only EthSEQ prediction did not match TCGA; and samples marked with “!” where only Ansextry prediction did not match TCGA. Genotypes were imputed from reference for Ansextry prediction when the corresponding locus had insufficient coverage. The median coverage across all samples was 91x, showing that most mispredicted samples had a median or above-median coverage, therefore, misprediction did not seem to be linked to lower-than-median coverage. Also, the median number of imputed genotypes for Ansextry classification across all samples was 390, which was close to the median of mispredicted Ansextry samples (393). Number of imputed genotypes across all 300 TCGA samples varied between 227 (min) and 690 (max), showing that 10- 15% imputed genotypes did not seem to have a negative impact on Ansextry prediction. TCGA self- declared Ansextry EthSEQ race prediction prediction Ansextry detailed prediction [%] black/afr. AMR AMR AFR(0.21)|AMR(90.53)|EAS(0.04)|EUR(7.75)|SAS(1.48) am. white AFR AFR AFR(99.94)|AMR(0.06)|EAS(0.0)|EUR(0.0)|SAS(0.0) black/afr. EUR AMR AFR(0.02)|AMR(17.04)|EAS(0.0)|EUR(82.76)|SAS(0.17) am. black/afr. AFR AMR AFR(68.03)|AMR(21.63)|EAS(0.2)|EUR(9.41)|SAS(0.73) am. white AMR EUR AFR(0.0)|AMR(54.79)|EAS(0.0)|EUR(45.1)|SAS(0.1) white AMR AMR AFR(0.01)|AMR(98.88)|EAS(0.01)|EUR(1.01)|SAS(0.08) white AFR AFR AFR(99.99)|AMR(0.0)|EAS(0.0)|EUR(0.0)|SAS(0.0) white AMR AMR AFR(0.01)|AMR(97.87)|EAS(0.11)|EUR(1.73)|SAS(0.27) white EUR AMR AFR(0.0)|AMR(0.84)|EAS(0.01)|EUR(98.92)|SAS(0.22) white EUR AMR AFR(0.0)|AMR(2.1)|EAS(0.0)|EUR(97.73)|SAS(0.15) white EUR AMR AFR(0.03)|AMR(31.14)|EAS(0.09)|EUR(65.73)|SAS(3.01) white EUR AMR AFR(0.01)|AMR(16.3)|EAS(0.01)|EUR(83.36)|SAS(0.33) white EUR AMR AFR(0.0)|AMR(0.44)|EAS(0.0)|EUR(99.38)|SAS(0.17) asian EUR EUR AFR(0.01)|AMR(3.12)|EAS(0.03)|EUR(95.6)|SAS(1.24) black/afr. EUR AMR AFR(28.14)|AMR(30.99)|EAS(0.36)|EUR(40.32)|SAS(0.18) am. black/afr. EUR EUR AFR(0.0)|AMR(0.01)|EAS(0.0)|EUR(99.93)|SAS(0.06) am. black/afr. EUR EUR AFR(0.0)|AMR(17.35)|EAS(0.0)|EUR(82.6)|SAS(0.05) am. black/afr. AFR AMR AFR(84.43)|AMR(15.38)|EAS(0.08)|EUR(0.09)|SAS(0.02) am. black/afr. AFR AMR AFR(60.73)|AMR(34.86)|EAS(0.25)|EUR(3.97)|SAS(0.19) am. TCGA Number of self- imputed declared EthSEQ detailed genotypes Mean race prediction [%] (Ansextry) coverage black/afr. n/a 410 81 am. white EUR(16.24)|AMR 295 121 (19.97)|SAS(17.76)|AFR(46.02) black/afr. n/a 393 97 am. black/afr. EUR(21.73)|EAS(9.16)|AMR(27.11)| 392 90 * am. SAS(23.21)|AFR(18.78) white n/a 330 156 ! white n/a 462 63 white n/a 322 124 white n/a 444 64 white n/a 263 181 * white n/a 412 132 * white n/a 325 121 * white n/a 410 109 * white n/a 302 113 * asian n/a 275 242 black/afr. EUR(21.12)|EAS(9.6)|AMR(25.78)| 479 59 am. SAS(22.41)|AFR(21.1) black/afr. n/a 319 122 am. black/afr. n/a 417 77 am. black/afr. EUR(19.18)|EAS(9.78)|AMR(25.38)| 333 114 * am. SAS(20.9)|AFR(24.77) black/afr. EUR(21.8)|EAS(9.45)|AMR(25.68)| 351 133 * am. SAS(22.5)|AFR(20.57)

Interestingly, the only individual misclassified by AnSextry and not by EthSEQ, which was categorized as white by TCGA, but predicted as AMR by the ancestry classifier, was actually predicted to be of admixed ancestry with a probability of 54.7% AMR and 45.1% EUR.

4 CONCLUSIONS

AnSextry, a novel method to reliably and easily determine the sex and ancestry of an individual based on aligned paired-end reads from whole-exome or, if target size permits, targeted sequencing experiments is presented. The tool provides a set of two Python-based classifiers relying on logistic regression, and the ancestry prediction represents an alternative approach to the mainly PCA-based methods used in the field of population genetics. AnSextry provides a ready-to-use reference model and requires minimal user input. It is fast, precise, and straightforward to use.

Disclaimer

Throughout this document the terms “ancestry-specifc”/“ethnicity-specific”/“population-specific” have been used interchangably, as different authors use different terms for the same purpose.

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Example 2

Using PHREGs as a Reference for NGS Read Mapping Increases Coverage of Clinically Relevant Biomarkers

We used 741 germline samples from GDC/TCGA [1] that were sequenced with whole-exome capture Illumina sequencing. This data set had 155 samples of African (AFR), 33 samples of Latino/admixed American (AMR), 179 samples of East Asian (EAS), 354 samples of European (EUR), and 20 samples of South Asian (SAS) ancestry. Each sample was aligned with Novoalign 4.00.01 to the standard human reference genome (HRG) GRCh37 [3], to the PHREG that was assigned by our ancestry classifier and to the HSA PHREG. The HSA PHREG was generated by aggregating the variant data over all GnomAD v2.1 ancestries [4], including AFR, AMR, EAS, EUR, and SAS.

For these read mapping strategies, we compared the coverage of 15,483 pathogenic ClinVar biomarkers version 2019-12 [5] in Gencode v31 CDS exons covering 1,288 genes [6]. We found increased coverage for 211 (AFR), 147 (AMR), 121 (EAS), 173 (EUR), 105 (SAS), and 162 (HSA) ClinVar biomarkers when aligning to the PHREG instead of the HRG (see Table 1). The majority of the variants with increased coverage were in vicinity of sites where the population-specific nucleotide was implanted in the PHREG. When mapping reads of a sample to its closest PHREG, the number of mismatches during alignment are reduced and thus coverage is increased, resulting in an elimination of the coverage drops when aligning to HRG.

In summary, our analysis indicates that the usage of the correct PHREG can increase the coverage and thus improve the detection of clinically relevant biomarkers.

TABLE 1 Caption Table 1 (ClinVar_PHREG_coverage_diff_relative.xlsx): List of ClinVar biomarkers (gene name|contig|start|end) in Gencode CDS exons that showed coverage differences when aligning to the PHREG compared to HRG. The difference is given relative to the coverage computed based on HRG alignments for each PHREG (AFR, AMR, EAS, EUR, SAS, HSA) as the median over the cases by ancestry and over all 741 cases (HSA). A positive number means increase in coverage, a negative number decrease in coverage. variant AFR AMR EAS EUR SAS HSA ABCD1|chrX|153006054|153006054 0.015 0 0 0 0 0 ABCD1|chrX|153006072|153006072 0.015 0 0 0 0 0 ABCD1|chrX|153006164|153006164 0.015 0 0 0 0 0 ABCD1|chrX|153006165|153006165 0.015 0 0 0 0 0 ABCD1|chrX|153008477|153008477 0 0.074 0 0.074 0 0.077 ABCD1|chrX|153008485|153008485 0 0.074 0 0.074 0 0.077 ABCD1|chrX|153008510|153008510 0 0.074 0 0.074 0 0.077 ALG1|chr16|5132566|5132566 0 0.025 0.016 0.013 0.018 0.021 ANKRD11|chr16|89345975|89345982 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89346103|89346103 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89349179|89349180 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89349245|89349248 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89349723|89349726 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89349751|89349752 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89349866|89349866 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89350538|89350541 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89350538|89350542 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89350549|89350552 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89350753|89350753 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89350772|89350775 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89350973|89350973 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89351043|89351047 0.01 0.008 0.009 0.008 0 0.01 ANKRD11|chr16|89351487|89351488 0.01 0.008 0.009 0.008 0 0.01 ATAD3A|chr1|1464679|1464679 0.455 0.727 0.561 0.133 0 0.958 ATM|chr11|108159703|108159703 0 0.01 0 0 0 0 ATM|chr11|108159705|108159705 0 0.01 0 0 0 0 ATM|chr11|108159737|108159737 0 0.01 0 0 0 0 ATM|chr11|108159792|108159792 0 0.01 0 0 0 0 ATM|chr11|108159821|108159821 0 0.01 0 0 0 0 BMPR1A|chr10|88635776|88635776 0.053 0.009 0.055 0 0.018 0.032 BMPR1A|chr10|88676897|88676897 0.102 0.124 0.108 0.113 0 0.11 BMPR1A|chr10|88676945|88676945 0.102 0.124 0.108 0.113 0 0.11 BMPR1A|chr10|88677032|88677032 0.102 0.124 0.108 0.113 0 0.11 BMPR1A|chr10|88677041|88677042 0.102 0.124 0.108 0.113 0 0.11 BMPR1A|chr10|88679141|88679141 0.067 −0.002 −0.002 −0.003 0 0.066 BMPR1A|chr10|88681331|88681331 0.018 0.012 0.014 0.014 0 0.015 BMPR1A|chr10|88683150|88683150 0.017 0.015 0.016 0 0 0 BMPR1A|chr10|88683357|88683357 0.042 0.054 0 0.065 0 0.064 BMPR1A|chr10|88683388|88683388 0.042 0.054 0 0.065 0 0.064 CFTR|chr7|117188696|117188696 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188719|117188723 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188725|117188725 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188786|117188792 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188815|117188815 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188825|117188825 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188843|117188843 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188849|117188849 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188850|117188851 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188852|117188852 0.133 0.133 0 0.165 0.18 0.162 CFTR|chr7|117188858|117188858 0.133 0.133 0 0.165 0.18 0.162 CYP11B1|chr8|143956669|143956669 0.145 0.098 0.386 0.059 0.013 0.127 CYP11B1|chr8|143957183|143957183 0.003 0.015 0.014 0 0 0.001 CYP11B1|chr8|143958438|143958438 0.194 0.088 0.225 0.134 0.158 0.184 CYP21A2|chr6|32006291|32006291 0.636 0.594 0.407 0.375 0.442 0.396 CYP21A2|chr6|32006858|32006858 0.027 0.155 0.048 0.146 0 0.146 CYP21A2|chr6|32006910|32006917 0.027 0.155 0.048 0.146 0 0.146 CYP21A2|chr6|32007203|32007203 0.024 0.145 0.027 0.128 −0.547 0.137 CYP21A2|chr6|32007887|32007887 −0.044 −0.218 0.022 −0.026 −0.032 −0.019 CYP21A2|chr6|32008500|32008500 −0.919 −0.538 −0.93 −0.928 0.418 −0.928 CYP21A2|chr6|32008783|32008783 −0.175 0.041 0.086 0.069 0.037 0.045 CYP21A2|chr6|32008870|32008870 −0.175 0.041 0.086 0.069 0.037 0.045 DCLRE1C|chr10|14976460|14976460 0.041 0.024 0.029 0.024 0.027 0.03 DUOX2|chr15|45403694|45403694 0.467 0 0 0.16 0 0 FLG|chr1|152277475|152277475 0.069 −0.01 0.027 0.013 −0.012 0.027 FLG|chr1|152280023|152280023 0.069 −0.01 0.027 0.013 −0.012 0.027 FLG|chr1|152280331|152280331 0.069 −0.01 0.027 0.013 −0.012 0.027 FLG|chr1|152281123|152281123 0.069 −0.01 0.027 0.013 −0.012 0.027 FLG|chr1|152283457|152283457 0.069 −0.01 0.027 0.013 −0.012 0.027 FLG|chr1|152285861|152285861 0.069 −0.01 0.027 0.013 −0.012 0.027 FLG|chr1|152286875|152286875 0.069 −0.01 0.027 0.013 −0.012 0.027 GBA|chr1|155205518|155205518 0.056 0.051 0.054 0.048 0.056 0.05 GBA|chr1|155205541|155205595 0.056 0.051 0.054 0.048 0.056 0.05 GBA|chr1|155205563|155205563 0.056 0.051 0.054 0.048 0.056 0.05 GBA|chr1|155205614|155205614 0.056 0.051 0.054 0.048 0.056 0.05 GBA|chr1|155208421|155208421 −0.683 0.003 −0.686 0 0 0 GLDC|chr9|6589230|6589230 0.017 0 0 0 0 0 GLUD1|chr10|88820766|88820766 0 0 0.027 0 0 0 HSPB1|chr7|75933395|75933395 0.047 0.033 0.027 0.037 0 0.041 HSPB1|chr7|75933411|75933411 0.047 0.033 0.027 0.037 0 0.041 KRT14|chr17|39742714|39742714 0.068 0.084 0.133 0.089 0.093 0.1 KRT16|chr17|39768562|39768562 0.076 0.06 0.055 0.072 0.071 0.069 KRT16|chr17|39768567|39768567 0.076 0.06 0.055 0.072 0.071 0.069 KRT17|chr17|39780487|39780487 0.007 −0.001 0 −0.002 −0.001 0.006 MT-ND1|chrM|3460|3460 0.013 0 0 0 0 0 MYH7|chr14|23889434|23889434 2.198 0.038 0.041 0.037 0.038 0.038 MYH7|chr14|23894969|23894969 0.019 0 0 0 0 0 MYH7|chr14|23894983|23894983 0.019 0 0 0 0 0 MYH7|chr14|23894999|23894999 0.019 0 0 0 0 0 MYH7|chr14|23895023|23895023 0.019 0 0 0 0 0 MYH7|chr14|23895027|23895027 0.019 0 0 0 0 0 OFD1|chrX|13767594|13767595 0 0 0 0.01 0 0.01 PIK3CA|chr3|178938934|178938934 0.026 0.02 0.032 0.02 0 0.02 PKD1|chr16|2153513|2153513 0.004 −0.006 −0.005 −0.005 0 −0.005 PKD1|chr16|2153747|2153747 0.004 −0.006 −0.005 −0.005 0 −0.005 PKD1|chr16|2156811|2156811 0.059 0 0 0 0 0.008 PKD1|chr16|2158440|2158441 0.002 0 0 0 0 0 PKD1|chr16|2158681|2158681 0.002 0 0 0 0 0 PKD1|chr16|2158969|2158969 0.002 0 0 0 0 0 PKD1|chr16|2159137|2159137 0.002 0 0 0 0 0 PKD1|chr16|2160153|2160154 0.002 0 0 0 0 0 PKD1|chr16|2164490|2164490 0.021 0.016 0.026 0.011 0.009 0.011 PKD1|chr16|2164809|2164809 0.021 0.016 0.026 0.011 0.009 0.011 PLEC|chr8|144994988|144994989 0.001 0 0 0 0 0 PMS2|chr7|6013113|6013113 3.649 0.4 3.567 0.5 4.198 2.771 PMS2|chr7|6017218|6017218 0.019 0 0 0 0 0 PMS2|chr7|6017251|6017251 0.019 0 0 0 0 0 PMS2|chr7|6017260|6017260 0.019 0 0 0 0 0 PMS2|chr7|6017300|6017303 0.019 0 0 0 0 0 PMS2|chr7|6022454|6022454 0.233 −0.253 0.514 −0.242 0 −0.154 PMS2|chr7|6022473|6022473 0.233 −0.253 0.514 −0.242 0 −0.154 PMS2|chr7|6022474|6022474 0.233 −0.253 0.514 −0.242 0 −0.154 PMS2|chr7|6022489|6022489 0.233 −0.253 0.514 −0.242 0 −0.154 PMS2|chr7|6022492|6022492 0.233 −0.253 0.514 −0.242 0 −0.154 PMS2|chr7|6022512|6022512 0.233 −0.253 0.514 −0.242 0 −0.154 PMS2|chr7|6022516|6022516 0.233 −0.253 0.514 −0.242 0 −0.154 PMS2|chr7|6026409|6026409 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026425|6026425 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026426|6026426 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026457|6026457 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026469|6026469 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026484|6026484 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026505|6026505 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026514|6026514 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026522|6026522 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026531|6026532 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026556|6026556 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026564|6026564 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026618|6026618 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026628|6026628 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026653|6026653 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026658|6026658 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026665|6026665 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026709|6026709 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026743|6026743 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026757|6026758 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026816|6026817 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026820|6026820 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026864|6026864 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026894|6026904 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026896|6026896 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026925|6026925 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6026968|6026971 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027020|6027020 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027064|6027064 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027089|6027089 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027099|6027099 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027117|6027121 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027135|6027135 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027156|6027156 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027175|6027175 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027190|6027190 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027215|6027215 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6027232|6027232 0.111 0.017 0.023 0.018 0.075 0.021 PMS2|chr7|6031643|6031643 0.024 −0.023 −0.018 0.03 0 0.029 PMS2|chr7|6031649|6031649 0.024 −0.023 −0.018 0.03 0 0.029 PRSS1|chr7|142458451|142458451 0.052 −0.023 −0.041 −0.042 −0.002 −0.021 PTEN|chr10|89720671|89720671 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720676|89720676 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720709|89720709 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720714|89720714 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720719|89720719 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720733|89720733 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720741|89720741 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720749|89720749 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720804|89720804 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720804|89720807 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720805|89720808 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720808|89720808 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720817|89720817 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720836|89720839 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720852|89720852 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720857|89720857 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720876|89720876 0 0.019 0 0.019 0.016 0.019 PTEN|chr10|89720877|89720877 0 0.019 0 0.019 0.016 0.019 PTPN11|chr12|112910758|112910758 0.006 0 0 0 0 0.006 PTPN11|chr12|112910765|112910765 0.006 0 0 0 0 0.006 PTPN11|chr12|112910772|112910772 0.006 0 0 0 0 0.006 PTPN11|chr12|112910776|112910776 0.006 0 0 0 0 0.006 PTPN11|chr12|112910785|112910785 0.006 0 0 0 0 0.006 PTPN11|chr12|112910793|112910793 0.006 0 0 0 0 0.006 PTPN11|chr12|112910827|112910827 0.006 0 0 0 0 0.006 PTPN11|chr12|112910835|112910835 0.006 0 0 0 0 0.006 PTPN11|chr12|112910837|112910837 0.006 0 0 0 0 0.006 PTPN11|chr12|112910844|112910844 0.006 0 0 0 0 0.006 SCN1A|chr2|166848059|166848059 0.013 0 0 0 0 0 SCN1A|chr2|166848111|166848111 0.013 0 0 0 0 0 SCN1A|chr2|166848129|166848129 0.013 0 0 0 0 0 SCN1A|chr2|166848230|166848230 0.013 0 0 0 0 0 SCN1A|chr2|166848246|166848249 0.013 0 0 0 0 0 SCN1A|chr2|166848437|166848437 0.013 0 0 0 0 0 SCN1A|chr2|166848438|166848438 0.013 0 0 0 0 0 SCN1A|chr2|166848563|166848563 0.013 0 0 0 0 0 SCN1A|chr2|166848772|166848775 0.013 0 0 0 0 0 SCN1A|chr2|166848788|166848788 0.013 0 0 0 0 0 SCN1A|chr2|166848800|166848800 0.013 0 0 0 0 0 SCN1A|chr2|166848851|166848851 0.013 0 0 0 0 0 SCN1A|chr2|166848878|166848878 0.013 0 0 0 0 0 SCN1A|chr2|166848879|166848879 0.013 0 0 0 0 0 SDHA|chr5|224547|224547 0.052 0.023 0 0 0 0 SDHA|chr5|226094|226094 0.024 0.079 0.019 0.078 0 0.081 SDHA|chr5|226156|226156 0.024 0.079 0.019 0.078 0 0.081 SDHA|chr5|235345|235345 0.007 0.004 0 0.006 0.002 0.005 SDHA|chr5|236714|236715 0.082 0 −0.013 −0.02 −0.016 −0.015 SDHA|chr5|240566|240567 0.026 0 0 0 0 0 SDHA|chr5|240574|240574 0.026 0 0 0 0 0 SDHA|chr5|251554|251554 0.172 0 0 0 0 0 SDHD|chr11|111965539|111965539 0 0 0 0.003 0 0 SDHD|chr11|111965551|111965554 0 0 0 0.003 0 0 SDHD|chr11|111965555|111965555 0 0 0 0.003 0 0 STRC|chr15|43896918|43896918 0.1 0 0 0 0 0 STRC|chr15|43896948|43896948 0.1 0 0 0 0 0 SUZ12|chr17|30267467|30267470 0.638 0 0 0 0 −0.457 TUBA1A|chr12|49578875|49578875 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49578884|49578884 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49578885|49578885 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49578923|49578923 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49578944|49578944 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49578945|49578945 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49578980|49578980 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49578981|49578981 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579001|49579001 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579044|49579044 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579053|49579053 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579163|49579163 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579190|49579190 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579229|49579229 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579341|49579341 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579359|49579359 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579508|49579508 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579668|49579668 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49579725|49579725 0.006 −0.03 −0.021 0.003 −0.016 −0.03 TUBA1A|chr12|49580100|49580100 0.006 0.013 0.024 0.009 0.014 0.014 TUBA1A|chr12|49580101|49580101 0.006 0.013 0.024 0.009 0.014 0.014 TUBA1A|chr12|49580116|49580116 0.006 0.013 0.024 0.009 0.014 0.014 TUBA1A|chr12|49580185|49580185 0.006 0.013 0.024 0.009 0.014 0.014 TUBA1A|chr12|49580430|49580430 0.006 0.013 0.024 0.009 0.014 0.014 TUBA1A|chr12|49580453|49580453 0.006 0.013 0.024 0.009 0.014 0.014 TUBA1A|chr12|49580541|49580541 0.006 0.013 0.024 0.009 0.014 0.014 TUBA1A|chr12|49580603|49580603 0.006 0.013 0.024 0.009 0.014 0.014 TUBA1A|chr12|49580615|49580615 0.006 0.013 0.024 0.009 0.014 0.014 TUBB2A|chr6|3154402|3154402 −0.054 −0.053 −0.088 0.109 −0.032 −0.022 TUBB2A|chr6|3154707|3154707 −0.054 −0.053 −0.088 0.109 −0.032 −0.022 TUBB2A|chr6|3155143|3155143 −0.054 −0.053 −0.088 0.109 −0.032 −0.022 VWF|chr12|6127701|6127701 0.014 0.004 0.027 0.023 0.029 0.006 VWF|chr12|6127795|6127795 0.014 0.004 0.027 0.023 0.029 0.006 VWF|chr12|6128449|6128449 0.014 0.004 0.027 0.023 0.029 0.006 VWF|chr12|6128463|6128463 0.014 0.004 0.027 0.023 0.029 0.006 VWF|chr12|6128464|6128464 0.014 0.004 0.027 0.023 0.029 0.006 VWF|chr12|6128638|6128638 0.014 0.004 0.027 0.023 0.029 0.006 VWF|chr12|6128662|6128662 0.014 0.004 0.027 0.023 0.029 0.006 VWF|chr12|6128668|6128668 0.014 0.004 0.027 0.023 0.029 0.006

REFERENCES FOR EXAMPLE 2

-   [1] https[://]portal.gdc.cancer.gov -   [2] http[://]www.novocraft.com/products/novoalign -   [3] https[://]www.ncbi.nlm.nih.gov/grc/human -   [4] https[://]gnomad.broadinstitute.org/faq -   [5] https[://]www.ncbi.nlm.nih.gov/clinvar -   [6] https[://]www.gencodegenes.org/human/release_31lift37.html

APPENDIX 1 chr1 1146964 1146965 A, G TNFRSF4 chr1 1147421 1147422 C, T TNFRSF4 chr1 1148099 1148100 C, G TNFRSF4 chr1 1148724 1148725 A, G TNFRSF4 chr1 1148820 1148821 A, G TNFRSF4 chr1 2488152 2488153 A, G TNFRSF14 chr1 2490512 2490513 C, G TNFRSF14 chr1 2491204 2491205 C, T TNFRSF14 chr1 2494329 2494330 A, G TNFRSF14 chr1 3598899 3598900 A, G TP73 chr1 3598909 3598910 C, T TP73 chr1 3599592 3599593 C, T TP73 chr1 3607519 3607520 A, G TP73 chr1 3607531 3607532 A, G TP73 chr1 3607605 3607606 A, C TP73 chr1 3638566 3638567 C, T TP73 chr1 3638592 3638593 A, G TP73 chr1 3638673 3638674 C, T TP73 chr1 3643680 3643681 A, G TP73 chr1 3643710 3643711 C, T TP73 chr1 3644290 3644291 A, C TP73 chr1 3644305 3644306 C, T TP73 chr1 3644321 3644322 A, G TP73 chr1 3644714 3644715 C, T TP73 chr1 3644753 3644754 C, T TP73 chr1 3644804 3644805 A, G TP73 chr1 3644857 3644858 C, G TP73 chr1 3645988 3645989 A, G TP73 chr1 3646517 3646518 A, G TP73 chr1 3647961 3647962 C, T TP73 chr1 3647972 3647973 A, G TP73 chr1 3649402 3649403 A, G TP73 chr1 3649420 3649421 C, T TP73 chr1 3649561 3649562 A, G TP73 chr1 7995089 7995090 G, T TNFRSF9 chr1 7999970 7999971 A, G TNFRSF9 chr1 8000024 8000025 A, G TNFRSF9 chr1 9775903 9775904 C, T PIK3CD chr1 9776574 9776575 A, G PIK3CD chr1 9776604 9776605 A, G PIK3CD chr1 9776714 9776715 A, C PIK3CD chr1 9777121 9777122 A, G PIK3CD chr1 9777665 9777666 C, T PIK3CD chr1 9777668 9777669 C, T PIK3CD chr1 9778765 9778766 C, T PIK3CD chr1 9780103 9780104 C, T PIK3CD chr1 9780195 9780196 A, G PIK3CD chr1 9780597 9780598 C, T PIK3CD chr1 9780761 9780762 A, G PIK3CD chr1 9780780 9780781 C, T PIK3CD chr1 9782260 9782261 C, T PIK3CD chr1 9782555 9782556 C, T PIK3CD chr1 9784422 9784423 C, T PIK3CD chr1 11167145 11167146 A, G MTOR chr1 11169271 11169272 A, G MTOR chr1 11169272 11169273 C, G MTOR chr1 11169675 11169676 C, T MTOR chr1 11172996 11172997 C, T MTOR chr1 11174849 11174850 C, T MTOR chr1 11174858 11174859 C, T MTOR chr1 11181326 11181327 C, T MTOR chr1 11181456 11181457 G, T MTOR chr1 11182062 11182063 A, G MTOR chr1 11190645 11190646 A, G MTOR chr1 11199447 11199448 C, T MTOR chr1 11205057 11205058 C, T MTOR chr1 11206689 11206690 A, T MTOR chr1 11272318 11272319 C, T MTOR chr1 11272467 11272468 C, G MTOR chr1 11288757 11288758 A, G MTOR chr1 11291511 11291512 A, G MTOR chr1 11293463 11293464 C, T MTOR chr1 11298582 11298583 A, G MTOR chr1 11300337 11300338 A, G MTOR chr1 11301713 11301714 A, G MTOR chr1 11308073 11308074 A, G MTOR chr1 11850926 11850927 C, T MTHFR chr1 11852299 11852300 C, T MTHFR chr1 11852302 11852303 A, G MTHFR chr1 11854017 11854018 C, T MTHFR chr1 11854456 11854457 A, G MTHFR chr1 11854475 11854476 G, T MTHFR chr1 11854754 11854755 A, G MTHFR chr1 11854895 11854896 A, G MTHFR chr1 11856377 11856378 A, G MTHFR chr1 11863056 11863057 A, G MTHFR chr1 11863565 11863566 G, T MTHFR chr1 12144433 12144434 A, G TNFRSF8 chr1 12157287 12157288 C, T TNFRSF8 chr1 12157320 12157321 C, G TNFRSF8 chr1 12169534 12169535 A, G TNFRSF8 chr1 12170286 12170287 C, T TNFRSF8 chr1 12172048 12172049 A, G TNFRSF8 chr1 12172124 12172125 C, T TNFRSF8 chr1 12186057 12186058 A, G TNFRSF8 chr1 12195660 12195661 A, G TNFRSF8 chr1 12195728 12195729 C, T TNFRSF8 chr1 15820447 15820448 G, T CASP9 chr1 15821958 15821959 A, G CASP9 chr1 15831271 15831272 C, T CASP9 chr1 15832542 15832543 C, T CASP9 chr1 15834359 15834360 A, G CASP9 chr1 15834490 15834491 A, G CASP9 chr1 15844925 15844926 C, T CASP9 chr1 15850602 15850603 A, G CASP9 chr1 15850612 15850613 A, G CASP9 chr1 16237806 16237807 A, G SPEN chr1 16242619 16242620 A, C SPEN chr1 16255643 16255644 C, T SPEN chr1 16256005 16256006 C, G SPEN chr1 16256006 16256007 C, T SPEN chr1 16257255 16257256 A, G SPEN chr1 16257644 16257645 C, T SPEN chr1 16259142 16259143 A, G SPEN chr1 16259812 16259813 A, G SPEN chr1 16260381 16260382 C, T SPEN chr1 16260391 16260392 A, G SPEN chr1 16260512 16260513 A, G SPEN chr1 16260915 16260916 C, T SPEN chr1 16262236 16262237 C, G SPEN chr1 16262355 16262356 C, T SPEN chr1 16262403 16262404 C, T SPEN chr1 16262718 16262719 C, T SPEN chr1 16264115 16264116 C, T SPEN chr1 20246986 20246987 C, T PLA2G2E chr1 20249252 20249253 A, G PLA2G2E chr1 20304925 20304926 A, G PLA2G2A chr1 20304961 20304962 C, G PLA2G2A chr1 20411331 20411332 C, T PLA2G5 chr1 20412722 20412723 A, G PLA2G5 chr1 20440782 20440783 C, T PLA2G2D chr1 20442053 20442054 C, T PLA2G2D chr1 20442073 20442074 C, T PLA2G2D chr1 20470147 20470148 C, T PLA2G2F chr1 20915700 20915701 A, C CDA chr1 20931448 20931449 A, G CDA chr1 20940257 20940258 A, T CDA chr1 25256048 25256049 C, T RUNX3 chr1 25291009 25291010 A, T RUNX3 chr1 26644536 26644537 A, C CD52 chr1 26646725 26646726 A, G CD52 chr1 26646729 26646730 A, G CD52 chr1 27057620 27057621 A, C ARID1A chr1 27100242 27100243 C, T ARID1A chr1 27102187 27102188 A, G ARID1A chr1 29138974 29138975 G, T OPRD1 chr1 29139048 29139049 A, G OPRD1 chr1 29139139 29139140 C, G OPRD1 chr1 29189482 29189483 C, T OPRD1 chr1 29189596 29189597 C, T OPRD1 chr1 29189600 29189601 A, G OPRD1 chr1 32790045 32790046 G, T HDAC1 chr1 32797240 32797241 C, G HDAC1 chr1 38289382 38289383 C, T MTF1 chr1 40363053 40363054 C, G MYCL1 chr1 40366647 40366648 A, G MYCL1 chr1 40367494 40367495 C, G MYCL1 chr1 43803669 43803670 A, G MPL chr1 43803806 43803807 G, T MPL chr1 43804339 43804340 A, G MPL chr1 43805239 43805240 A, G MPL chr1 45291907 45291908 A, G PTCH2 chr1 45292172 45292173 A, G PTCH2 chr1 45292482 45292483 C, T PTCH2 chr1 45292703 45292704 A, G PTCH2 chr1 45292865 45292866 A, G PTCH2 chr1 45293056 45293057 A, G PTCH2 chr1 45293089 45293090 A, G PTCH2 chr1 45293517 45293518 A, G PTCH2 chr1 45294143 45294144 C, T PTCH2 chr1 45294155 45294156 C, T PTCH2 chr1 45296645 45296646 A, G PTCH2 chr1 45297752 45297753 A, C, G PTCH2 chr1 45307505 45307506 A, G PTCH2 chr1 45308616 45308617 C, G PTCH2 chr1 45795026 45795027 C, T MUTYH chr1 45796114 45796115 A, G MUTYH chr1 45796898 45796899 C, G MUTYH chr1 45798509 45798510 C, T MUTYH chr1 45800032 45800033 C, T MUTYH chr1 45800155 45800156 C, T MUTYH chr1 45805623 45805624 A, G MUTYH chr1 47264946 47264947 A, G CYP4B1 chr1 47276727 47276728 C, G CYP4B1 chr1 47276818 47276819 A, G CYP4B1 chr1 47276839 47276840 C, T CYP4B1 chr1 47276883 47276884 G, T CYP4B1 chr1 47276938 47276939 A, G CYP4B1 chr1 47278168 47278169 A, G CYP4B1 chr1 47279099 47279100 C, G CYP4B1 chr1 47279175 47279176 A, G CYP4B1 chr1 47279836 47279837 A, G CYP4B1 chr1 47279897 47279898 C, T CYP4B1 chr1 47280851 47280852 A, C CYP4B1 chr1 47280858 47280859 A, G CYP4B1 chr1 47280883 47280884 C, T CYP4B1 chr1 47282702 47282703 G, T CYP4B1 chr1 47282754 47282755 C, G CYP4B1 chr1 47282771 47282772 C, T CYP4B1 chr1 47283626 47283627 C, T CYP4B1 chr1 47284242 47284243 C, T CYP4B1 chr1 47284394 47284395 A, G CYP4B1 chr1 59247992 59247993 C, T JUN chr1 59248220 59248221 A, G JUN chr1 65301764 65301765 G, T JAK1 chr1 65303646 65303647 A, G JAK1 chr1 65303658 65303659 C, T JAK1 chr1 65303661 65303662 A, G JAK1 chr1 65310488 65310489 C, T JAK1 chr1 65311213 65311214 C, G JAK1 chr1 65311261 65311262 A, G JAK1 chr1 65312341 65312342 A, G JAK1 chr1 65321249 65321250 A, G JAK1 chr1 65321387 65321388 A, G JAK1 chr1 65321408 65321409 C, T JAK1 chr1 65321418 65321419 A, G JAK1 chr1 65325969 65325970 C, T JAK1 chr1 65332626 65332627 C, T JAK1 chr1 65335061 65335062 A, G JAK1 chr1 65335094 65335095 C, T JAK1 chr1 65339121 65339122 G JAK1 chr1 65351895 65351896 C, T JAK1 chr1 68896897 68896898 A, G RPE65 chr1 68896944 68896945 G, T RPE65 chr1 68897000 68897001 C, G, T RPE65 chr1 68897001 68897002 A, G RPE65 chr1 68903941 68903942 C, T RPE65 chr1 68904659 68904660 A, C RPE65 chr1 68904741 68904742 G, T RPE65 chr1 68904786 68904787 C, T RPE65 chr1 68905357 68905358 C, G RPE65 chr1 68910309 68910310 A, G RPE65 chr1 68910314 68910315 C, T RPE65 chr1 91973799 91973800 G, T CDC7 chr1 91977393 91977394 C, G CDC7 chr1 91981483 91981484 A, G CDC7 chr1 91989706 91989707 A, G CDC7 chr1 95001599 95001600 A, C F3 chr1 95001654 95001655 C, T F3 chr1 95005757 95005758 A, G F3 chr1 95007260 95007261 G, T F3 chr1 97544542 97544543 G, T DPYD chr1 97770919 97770920 C, T DPYD chr1 97848040 97848041 G, T DPYD chr1 97915623 97915624 A, G DPYD chr1 97981394 97981395 C, T DPYD chr1 97981420 97981421 C, T DPYD chr1 97981507 97981508 C, T DPYD chr1 98015145 98015146 C, T DPYD chr1 98039436 98039437 C, T DPYD chr1 98060752 98060753 A, G DPYD chr1 98157361 98157362 A, G DPYD chr1 98165090 98165091 C, T DPYD chr1 98348884 98348885 A, G DPYD chr1 101185362 101185363 A, G VCAM1 chr1 101190172 101190173 C, T VCAM1 chr1 101194686 101194687 C, T VCAM1 chr1 101194883 101194884 A, G VCAM1 chr1 101196786 101196787 C, G VCAM1 chr1 101197011 101197012 A, G VCAM1 chr1 101203764 101203765 A, T VCAM1 chr1 101203826 101203827 A, G VCAM1 chr1 101704571 101704572 A, C S1PR1 chr1 113456545 113456546 A, T SLC16A1 chr1 115829202 115829203 C, T NGF chr1 115829243 115829244 A, G NGF chr1 115829312 115829313 A, G NGF chr1 115829362 115829363 C, T NGF chr1 118165576 118165577 C, G FAM46C chr1 118165690 118165691 C, G, T FAM46C chr1 118165972 118165973 C, T FAM46C chr1 118166095 118166096 C, T FAM46C chr1 118166194 118166195 C, T FAM46C chr1 120458003 120458004 A, T NOTCH2 chr1 120458923 120458924 A, G NOTCH2 chr1 120463043 120463044 C, T NOTCH2 chr1 120465006 120465007 A, T NOTCH2 chr1 120468127 120468128 A, G NOTCH2 chr1 120468133 120468134 C, T NOTCH2 chr1 120468424 120468425 A, G NOTCH2 chr1 120468486 120468487 C, T NOTCH2 chr1 120469146 120469147 C, T NOTCH2 chr1 120471856 120471857 C, T NOTCH2 chr1 120480582 120480583 A, G NOTCH2 chr1 120483243 120483244 C, T NOTCH2 chr1 120484420 120484421 A, G NOTCH2 chr1 120491617 120491618 C, G NOTCH2 chr1 120512302 120512303 A, G NOTCH2 chr1 120548151 120548152 C, T NOTCH2 chr1 120611559 120611560 C, T NOTCH2 chr1 120612005 120612006 A, G NOTCH2 chr1 150551294 150551295 C, T MCL1 chr1 150551418 150551419 C, T MCL1 chr1 155023997 155023998 G, T ADAM15 chr1 155026374 155026375 C, T ADAM15 chr1 155026870 155026871 G, T ADAM15 chr1 155026941 155026942 A, C ADAM15 chr1 155028449 155028450 A, C ADAM15 chr1 155028521 155028522 A, G ADAM15 chr1 155029747 155029748 C, T ADAM15 chr1 155030556 155030557 A, C ADAM15 chr1 155030970 155030971 A, G ADAM15 chr1 155032751 155032752 A, G ADAM15 chr1 155033307 155033308 A, G ADAM15 chr1 155033316 155033317 C, T ADAM15 chr1 155033917 155033918 C, T ADAM15 chr1 156212566 156212567 A, C BGLAP chr1 156212925 156212926 C, G BGLAP chr1 156212930 156212931 A, G BGLAP chr1 156785616 156785617 A, G NTRK1 chr1 156834511 156834512 C, T NTRK1 chr1 156837846 156837847 C, T NTRK1 chr1 156838431 156838432 C, T NTRK1 chr1 156843653 156843654 A, G NTRK1 chr1 156844776 156844777 A, G NTRK1 chr1 156846232 156846233 A, G NTRK1 chr1 156848917 156848918 C, T NTRK1 chr1 156848945 156848946 G, T NTRK1 chr1 156848967 156848968 C, T NTRK1 chr1 156848994 156848995 C, T NTRK1 chr1 156849795 156849796 A, G NTRK1 chr1 156849945 156849946 A, G NTRK1 chr1 162688808 162688809 A, G DDR2 chr1 162722845 162722846 C, G DDR2 chr1 162722880 162722881 C, T DDR2 chr1 162725037 162725038 C, T DDR2 chr1 162731255 162731256 A, C DDR2 chr1 162737115 162737116 C, G DDR2 chr1 162740312 162740313 C, T DDR2 chr1 162740326 162740327 C, T DDR2 chr1 162743417 162743418 G, T DDR2 chr1 162749948 162749949 G, T DDR2 chr1 169483560 169483561 C, T F5 chr1 169484766 169484767 A, G F5 chr1 169487820 169487821 G, T F5 chr1 169489721 169489722 A, G F5 chr1 169492614 169492615 C, T F5 chr1 169497291 169497292 C, T F5 chr1 169498974 169498975 C, T F5 chr1 169500209 169500210 C, T F5 chr1 169510117 169510118 A, G F5 chr1 169510138 169510139 A, G F5 chr1 169510347 169510348 C, T F5 chr1 169510375 169510376 G, T F5 chr1 169510379 169510380 A, G F5 chr1 169510823 169510824 G, T F5 chr1 169510889 169510890 C, G F5 chr1 169511554 169511555 C, T F5 chr1 169511733 169511734 C, T F5 chr1 169511754 169511755 C, T F5 chr1 169511877 169511878 G, T F5 chr1 169511902 169511903 A, G F5 chr1 169512026 169512027 C, T F5 chr1 169512038 169512039 C, T F5 chr1 169512092 169512093 A, G F5 chr1 169512119 169512120 A, G F5 chr1 169512222 169512223 A, G F5 chr1 169513582 169513583 G, T F5 chr1 169515725 169515726 C, T F5 chr1 169519111 169519112 C, T F5 chr1 169519893 169519894 A, G F5 chr1 169521852 169521853 A, G F5 chr1 169526019 169526020 A, G F5 chr1 169528579 169528580 C, T F5 chr1 169529754 169529755 A, G F5 chr1 169529813 169529814 C, G F5 chr1 169529825 169529826 A, C F5 chr1 169541512 169541513 C, G F5 chr1 169541619 169541620 A, G F5 chr1 169551681 169551682 C, T F5 chr1 169555453 169555454 A, G F5 chr1 169555581 169555582 C, T F5 chr1 169560612 169560613 A, T SELP chr1 169562903 169562904 C, T SELP chr1 169562948 169562949 A, G SELP chr1 169563950 169563951 G, T SELP chr1 169565245 169565246 C, T SELP chr1 169565283 169565284 C, T SELP chr1 169565345 169565346 A, C SELP chr1 169565392 169565393 A, C SELP chr1 169566241 169566242 C, T SELP chr1 169566264 169566265 A, C SELP chr1 169566307 169566308 A, G SELP chr1 169566312 169566313 C, T SELP chr1 169566325 169566326 A, G SELP chr1 169566328 169566329 A, G SELP chr1 169576374 169576375 A, G SELP chr1 169580884 169580885 C, T SELP chr1 169581594 169581595 A, G SELP chr1 169582316 169582317 C, T SELP chr1 169586668 169586669 G, T SELP chr1 169588353 169588354 A, G SELP chr1 169599253 169599254 C, T SELP chr1 169660938 169660939 C, T SELL chr1 169665631 169665632 C, T SELL chr1 169676485 169676486 A, G SELL chr1 169677678 169677679 A, G SELL chr1 169677981 169677982 A, T SELL chr1 169679552 169679553 C, T SELL chr1 172628487 172628488 A, G FASLG chr1 172628620 172628621 G, T FASLG chr1 172633610 172633611 C, G FASLG chr1 179077557 179077558 A, G ABL2 chr1 179078196 179078197 A, C ABL2 chr1 179078590 179078591 C, T ABL2 chr1 179084079 179084080 G, T ABL2 chr1 179090750 179090751 C, T ABL2 chr1 179095547 179095548 C, T ABL2 chr1 179112109 179112110 G, T ABL2 chr1 179112144 179112145 C, G ABL2 chr1 183532436 183532437 A, G NCF2 chr1 183532444 183532445 C, G NCF2 chr1 183532471 183532472 C NCF2 chr1 183532579 183532580 G, T NCF2 chr1 183533216 183533217 C NCF2 chr1 183534934 183534935 C, T NCF2 chr1 183534944 183534945 C, T NCF2 chr1 183536088 183536089 A, G NCF2 chr1 183542386 183542387 C, T NCF2 chr1 183555962 183555963 C, T NCF2 chr1 186643540 186643541 C, T PTGS2 chr1 186643767 186643768 A, G PTGS2 chr1 186645077 186645078 A, G PTGS2 chr1 186645668 186645669 A, G PTGS2 chr1 186645926 186645927 C, T PTGS2 chr1 186648354 186648355 C, G PTGS2 chr1 193117123 193117124 A, T CDC73 chr1 193173025 193173026 A, G CDC73 chr1 193202152 193202153 A, G CDC73 chr1 197008596 197008597 A, C F13B chr1 197009797 197009798 A, G F13B chr1 197019857 197019858 A, C F13B chr1 197019978 197019979 A, G F13B chr1 197026264 197026265 C, T F13B chr1 197031020 197031021 C, T F13B chr1 198661414 198661415 A, G PTPRC chr1 198671652 198671653 A, G PTPRC chr1 198672538 198672539 A, G PTPRC chr1 198678833 198678834 A, G PTPRC chr1 198682057 198682058 A, G PTPRC chr1 198704293 198704294 C, T PTPRC chr1 198711166 198711167 A, G PTPRC chr1 198718691 198718692 C, T PTPRC chr1 198725168 198725169 C, T PTPRC chr1 204494737 204494738 A, G MDM4 chr1 204501382 204501383 C, T MDM4 chr1 204506106 204506107 C, T MDM4 chr1 204511923 204511924 C, T MDM4 chr1 204515941 204515942 A MDM4 chr1 204516024 204516025 A, G MDM4 chr1 204518245 204518246 A, G MDM4 chr1 204518740 204518741 A, G MDM4 chr1 206647786 206647787 C, T IKBKE chr1 206647843 206647844 C, T IKBKE chr1 206649680 206649681 A, G IKBKE chr1 206650064 206650065 A, G IKBKE chr1 206651106 206651107 A, G IKBKE chr1 206651595 206651596 C, T IKBKE chr1 206651724 206651725 C, T IKBKE chr1 206652403 206652404 A, G IKBKE chr1 206652499 206652500 A, G IKBKE chr1 206652523 206652524 C, T IKBKE chr1 206661262 206661263 T IKBKE chr1 206665051 206665052 C, T IKBKE chr1 206666280 206666281 C, T IKBKE chr1 206666583 206666584 A, G IKBKE chr1 206666733 206666734 G, T IKBKE chr1 206669398 206669399 C, G IKBKE chr1 206669441 206669442 C, T IKBKE chr1 206669464 206669465 C, T IKBKE chr1 223284527 223284528 A, G TLR5 chr1 223284598 223284599 C, T TLR5 chr1 223285041 223285042 A, G TLR5 chr1 223285506 223285507 G, T TLR5 chr1 223285945 223285946 G, T TLR5 chr1 223286039 223286040 C, G TLR5 chr1 226550740 226550741 C, T PARP1 chr1 226550828 226550829 C, T PARP1 chr1 226550923 226550924 C, G PARP1 chr1 226553579 226553580 A, G PARP1 chr1 226555301 226555302 A, G PARP1 chr1 226555347 226555348 A, G PARP1 chr1 226564835 226564836 A, G PARP1 chr1 226565048 226565049 G, T PARP1 chr1 226566958 226566959 C PARP1 chr1 226567007 226567008 C, G PARP1 chr1 226567026 226567027 A, G PARP1 chr1 226567171 226567172 A, C PARP1 chr1 226567191 226567192 C, T PARP1 chr1 226567240 226567241 C, T PARP1 chr1 226570839 226570840 C, T PARP1 chr1 226573363 226573364 A, G PARP1 chr1 226573401 226573402 C, T PARP1 chr1 226573984 226573985 C, T PARP1 chr1 226576269 226576270 A, G PARP1 chr1 226576295 226576296 A, G PARP1 chr1 226576334 226576335 A, G PARP1 chr1 226576335 226576336 A, G PARP1 chr1 226580020 226580021 G, T PARP1 chr1 226580052 226580053 G, T PARP1 chr1 226589708 226589709 C, T PARP1 chr1 226589832 226589833 C, T PARP1 chr1 226589857 226589858 C PARP1 chr1 226595646 226595647 C, G PARP1 chr1 236958682 236958683 C, G MTR chr1 236958936 236958937 C, T MTR chr1 236971982 236971983 C, T MTR chr1 236971997 236971998 C, T MTR chr1 236975053 236975054 C, G MTR chr1 236990140 236990141 A, G MTR chr1 237038160 237038161 C, T MTR chr1 237038220 237038221 C, G MTR chr1 237048499 237048500 A, G MTR chr1 237048515 237048516 C, G MTR chr1 237054565 237054566 C, T MTR chr1 237054568 237054569 A, G MTR chr1 237058728 237058729 C, T MTR chr1 237058742 237058743 A, G MTR chr1 237058743 237058744 A, C MTR chr1 237058747 237058748 C, T MTR chr1 237060294 237060295 A, G MTR chr1 237060295 237060296 A, C MTR chr1 237060371 237060372 A, G MTR chr1 237060432 237060433 G, T MTR chr1 237060849 237060850 C, T MTR chr1 237060996 237060997 A, G MTR chr2 10262858 10262859 A, G RRM2 chr2 10262864 10262865 C, G RRM2 chr2 10262891 10262892 C, T RRM2 chr2 10262919 10262920 G, T RRM2 chr2 10267210 10267211 C, T RRM2 chr2 11323530 11323531 A, C ROCK2 chr2 11323540 11323541 C, T ROCK2 chr2 11334383 11334384 G, T ROCK2 chr2 11347940 11347941 G, T ROCK2 chr2 11351864 11351865 C, T ROCK2 chr2 11355232 11355233 A, G ROCK2 chr2 11359119 11359120 G, T ROCK2 chr2 11389813 11389814 A, G ROCK2 chr2 11389906 11389907 C, T ROCK2 chr2 11426622 11426623 C, T ROCK2 chr2 11426733 11426734 C, T ROCK2 chr2 11427886 11427887 A, T ROCK2 chr2 11484095 11484096 C, G ROCK2 chr2 25457198 25457199 C, T DNMT3A chr2 25457350 25457351 C, T DNMT3A chr2 25458545 25458546 C, T DNMT3A chr2 25462326 25462327 C, G DNMT3A chr2 25469184 25469185 G DNMT3A chr2 25469501 25469502 C, T DNMT3A chr2 25469627 25469628 C, T DNMT3A chr2 25471001 25471002 A, G DNMT3A chr2 25475036 25475037 A, C DNMT3A chr2 25523064 25523065 C, T DNMT3A chr2 29416356 29416357 A, G ALK chr2 29416365 29416366 C, G ALK chr2 29416480 29416481 C, T ALK chr2 29416571 29416572 C, T ALK chr2 29416614 29416615 A, G ALK chr2 29416749 29416750 A, G ALK chr2 29416793 29416794 A, G ALK chr2 29420549 29420550 C, T ALK chr2 29430757 29430758 A, G ALK chr2 29432775 29432776 C, T ALK chr2 29443616 29443617 C, G ALK chr2 29443748 29443749 G, T ALK chr2 29444075 29444076 G, T ALK chr2 29444094 29444095 C, T ALK chr2 29445156 29445157 C, G ALK chr2 29445424 29445425 A, G ALK chr2 29446201 29446202 A, G ALK chr2 29450372 29450373 A, T ALK chr2 29455266 29455267 A, G ALK chr2 29473999 29474000 A, G ALK chr2 29474041 29474042 A, G ALK chr2 29497920 29497921 A, C ALK chr2 29497994 29497995 A, G ALK chr2 29519714 29519715 C, T ALK chr2 29519851 29519852 A, G ALK chr2 29541103 29541104 C, T ALK chr2 29543662 29543663 C, T ALK chr2 29543735 29543736 A, G ALK chr2 29543773 29543774 C, T ALK chr2 29754824 29754825 C ALK chr2 29940528 29940529 A, T ALK chr2 30142880 30142881 A, G ALK chr2 38298138 38298139 C, T CYP1B1 chr2 38298149 38298150 A, G CYP1B1 chr2 38298168 38298169 C, G CYP1B1 chr2 38298202 38298203 C, G CYP1B1 chr2 38298393 38298394 C, T CYP1B1 chr2 38301802 38301803 C, G CYP1B1 chr2 38301846 38301847 C, T CYP1B1 chr2 38301937 38301938 A, G CYP1B1 chr2 38302176 38302177 A, C CYP1B1 chr2 38302389 38302390 C, G CYP1B1 chr2 42396721 42396722 A, G EML4 chr2 42491940 42491941 C, T EML4 chr2 42491950 42491951 C, T EML4 chr2 42491996 42491997 A, G EML4 chr2 42508047 42508048 C, T EML4 chr2 42508151 42508152 C, G EML4 chr2 42510177 42510178 C, T EML4 chr2 42511902 42511903 A, G EML4 chr2 42515387 42515388 A, G EML4 chr2 42515436 42515437 A, G EML4 chr2 42515500 42515501 C, T EML4 chr2 42531706 42531707 C, G EML4 chr2 42531716 42531717 A, G EML4 chr2 42552283 42552284 C, G EML4 chr2 42552407 42552408 A, G EML4 chr2 42556021 42556022 A, T EML4 chr2 42557333 42557334 C, T EML4 chr2 47380144 47380145 C, T CALM2 chr2 47380202 47380203 C, T CALM2 chr2 47399600 47399601 A, G CALM2 chr2 47596199 47596200 A, G EPCAM chr2 47600765 47600766 C, T EPCAM chr2 47601105 47601106 C, T EPCAM chr2 47604175 47604176 C, T EPCAM chr2 47604277 47604278 A, G EPCAM chr2 47612223 47612224 C, T EPCAM chr2 47612297 47612298 C, T EPCAM chr2 47612298 47612299 A, G EPCAM chr2 47613698 47613699 C, T EPCAM chr2 47613787 47613788 A, G EPCAM chr2 47637245 47637246 A, G MSH2 chr2 47637438 47637439 C, T MSH2 chr2 47643475 47643476 C, T MSH2 chr2 47693787 47693788 A, T MSH2 chr2 47698094 47698095 A, G MSH2 chr2 47710048 47710049 C, T MSH2 chr2 47739550 47739551 A, G MSH2 chr2 48010487 48010488 A, G MSH6 chr2 48010557 48010558 A, C MSH6 chr2 48018080 48018081 A, G MSH6 chr2 48023114 48023115 C, T MSH6 chr2 48025763 48025764 C, T MSH6 chr2 48026285 48026286 C, T MSH6 chr2 48027374 48027375 C, T MSH6 chr2 48027393 48027394 C, T MSH6 chr2 48030691 48030692 A, T MSH6 chr2 48033550 48033551 C, G MSH6 chr2 48915266 48915267 C, T LHCGR chr2 48915870 48915871 A, G LHCGR chr2 48921374 48921375 C, T LHCGR chr2 48921437 48921438 C, T LHCGR chr2 48925745 48925746 C, T LHCGR chr2 48948855 48948856 A, G LHCGR chr2 48948977 48948978 A, G LHCGR chr2 48956416 48956417 C, T LHCGR chr2 48956430 48956431 A, T LHCGR chr2 48982621 48982622 C, G LHCGR chr2 55460086 55460087 A, G RPS27A chr2 58388695 58388696 A, G FANCL chr2 58390513 58390514 C, G FANCL chr2 58390537 58390538 C, T FANCL chr2 58390546 58390547 A, G FANCL chr2 58390588 58390589 A, C FANCL chr2 58421265 58421266 C, T FANCL chr2 58431409 58431410 C, G FANCL chr2 58431445 58431446 C, T FANCL chr2 58453929 58453930 A, G FANCL chr2 58453962 58453963 A, T FANCL chr2 61709488 61709489 C, G XPO1 chr2 61710076 61710077 A, G XPO1 chr2 61711210 61711211 C, T XPO1 chr2 61715323 61715324 C, T XPO1 chr2 61722723 61722724 G, T XPO1 chr2 61729229 61729230 C, T XPO1 chr2 61749721 61749722 A, C XPO1 chr2 69093287 69093288 G, T BMP10 chr2 69093311 69093312 A, G BMP10 chr2 75276648 75276649 C, T TACR1 chr2 75276858 75276859 C, T TACR1 chr2 75425727 75425728 A, G TACR1 chr2 75426070 75426071 G TACR1 chr2 108994807 108994808 C, G SULT1C4 chr2 108998211 108998212 C, T SULT1C4 chr2 108998797 108998798 A, G, T SULT1C4 chr2 108999785 108999786 C, T SULT1C4 chr2 109003716 109003717 G, T SULT1C4 chr2 109003760 109003761 A, G SULT1C4 chr2 111397344 111397345 C, T BUB1 chr2 111419352 111419353 C, T BUB1 chr2 111419425 111419426 A, G BUB1 chr2 111423829 111423830 C, T BUB1 chr2 111430380 111430381 A, C BUB1 chr2 111431950 111431951 C, G BUB1 chr2 113532884 113532885 G, T IL1A chr2 113537150 113537151 C, T IL1A chr2 113539223 113539224 A, G IL1A chr2 113540412 113540413 A, G IL1A chr2 113541381 113541382 C, T IL1A chr2 140992322 140992323 C, T LRP1B chr2 140992336 140992337 A, C LRP1B chr2 140992346 140992347 C, T LRP1B chr2 141027925 141027926 A, G LRP1B chr2 141032087 141032088 C, T LRP1B chr2 141079616 141079617 A, G LRP1B chr2 141108530 141108531 A, G LRP1B chr2 141110676 141110677 A, C LRP1B chr2 141130694 141130695 C, T LRP1B chr2 141242917 141242918 C, T LRP1B chr2 141245160 141245161 C, T LRP1B chr2 141259375 141259376 A, G LRP1B chr2 141260667 141260668 A, G LRP1B chr2 141267572 141267573 A, G LRP1B chr2 141272252 141272253 C, T LRP1B chr2 141274563 141274564 C, T LRP1B chr2 141274575 141274576 C, T LRP1B chr2 141283400 141283401 A, T LRP1B chr2 141283424 141283425 A, G LRP1B chr2 141294249 141294250 C, T LRP1B chr2 141298673 141298674 C, T LRP1B chr2 141298681 141298682 C, G LRP1B chr2 141457961 141457962 C, T LRP1B chr2 141457984 141457985 A, T LRP1B chr2 141459963 141459964 C, T LRP1B chr2 141473504 141473505 A, T LRP1B chr2 141526813 141526814 C, G LRP1B chr2 141528434 141528435 C, T LRP1B chr2 141528442 141528443 C, T LRP1B chr2 141533661 141533662 C, T LRP1B chr2 141571328 141571329 C, T LRP1B chr2 141625345 141625346 C, T LRP1B chr2 141680637 141680638 C, T LRP1B chr2 141707867 141707868 G, T LRP1B chr2 141707982 141707983 C, T LRP1B chr2 141708020 141708021 A, T LRP1B chr2 141709405 141709406 G, T LRP1B chr2 141709418 141709419 G, T LRP1B chr2 141747248 141747249 A, T LRP1B chr2 141751591 141751592 A, G LRP1B chr2 141751675 141751676 C, T LRP1B chr2 141763011 141763012 G, T LRP1B chr2 141763070 141763071 A, G LRP1B chr2 141771115 141771116 C, T LRP1B chr2 141773396 141773397 A, C LRP1B chr2 141816494 141816495 A, G LRP1B chr2 141946093 141946094 A, G LRP1B chr2 141946168 141946169 A, C LRP1B chr2 141946176 141946177 G, T LRP1B chr2 142012035 142012036 G, T LRP1B chr2 142567909 142567910 C, T LRP1B chr2 145147191 145147192 G ZEB2 chr2 145156550 145156551 A, G ZEB2 chr2 145157823 145157824 A, G ZEB2 chr2 145161479 145161480 C ZEB2 chr2 145255209 145255210 C, T ZEB2 chr2 160958342 160958343 C, T ITGB6 chr2 160968627 160968628 A, G ITGB6 chr2 160994292 160994293 C, T ITGB6 chr2 160994347 160994348 C, T ITGB6 chr2 160994408 160994409 C, T ITGB6 chr2 161029217 161029218 A, G ITGB6 chr2 161030526 161030527 C, G ITGB6 chr2 161051852 161051853 A, G ITGB6 chr2 162862391 162862392 G, T DPP4 chr2 162865067 162865068 A, G DPP4 chr2 162865132 162865133 C, T DPP4 chr2 162865822 162865823 A, T DPP4 chr2 162875348 162875349 C, G DPP4 chr2 162875842 162875843 A, C DPP4 chr2 162876767 162876768 A, G DPP4 chr2 162881474 162881475 C, G DPP4 chr2 162903311 162903312 C, T DPP4 chr2 162903409 162903410 C, T DPP4 chr2 162929921 162929922 C, T DPP4 chr2 162929978 162929979 A, G DPP4 chr2 169985619 169985620 A, C LRP2 chr2 169993976 169993977 C LRP2 chr2 169996936 169996937 C, T LRP2 chr2 169997008 169997009 A, G LRP2 chr2 169997029 169997030 C, G LRP2 chr2 169997050 169997051 A, G LRP2 chr2 170003431 170003432 G, T LRP2 chr2 170003507 170003508 A, G LRP2 chr2 170010984 170010985 C, T LRP2 chr2 170012779 170012780 A, G LRP2 chr2 170019114 170019115 A, C LRP2 chr2 170019120 170019121 A, C LRP2 chr2 170025082 170025083 A, G LRP2 chr2 170027094 170027095 A, G LRP2 chr2 170031823 170031824 C, T LRP2 chr2 170032988 170032989 C, T LRP2 chr2 170033088 170033089 A, G LRP2 chr2 170038760 170038761 C, T LRP2 chr2 170048555 170048556 C LRP2 chr2 170053504 170053505 C, T LRP2 chr2 170055254 170055255 C, T LRP2 chr2 170062077 170062078 C, G LRP2 chr2 170063419 170063420 C, T LRP2 chr2 170063470 170063471 A, G LRP2 chr2 170068490 170068491 C, T LRP2 chr2 170068712 170068713 A, G LRP2 chr2 170070347 170070348 C, T LRP2 chr2 170072886 170072887 C, G LRP2 chr2 170082012 170082013 A, G LRP2 chr2 170083032 170083033 C, T LRP2 chr2 170088350 170088351 A, G LRP2 chr2 170092394 170092395 A, G LRP2 chr2 170092601 170092602 A, G LRP2 chr2 170092612 170092613 C, G LRP2 chr2 170094762 170094763 C, G LRP2 chr2 170096017 170096018 A, G LRP2 chr2 170096094 170096095 C, G LRP2 chr2 170096290 170096291 A, G LRP2 chr2 170097706 170097707 G, T LRP2 chr2 170099445 170099446 G, T LRP2 chr2 170099452 170099453 A, T LRP2 chr2 170099472 170099473 C, T LRP2 chr2 170099473 170099474 A, G LRP2 chr2 170103335 170103336 C, T LRP2 chr2 170103350 170103351 G, T LRP2 chr2 170112659 170112660 C, T LRP2 chr2 170115587 170115588 C, T LRP2 chr2 170115671 170115672 A, G LRP2 chr2 170129527 170129528 A, G LRP2 chr2 170129528 170129529 A, G LRP2 chr2 170139345 170139346 C, T LRP2 chr2 170139386 170139387 A, C LRP2 chr2 170145660 170145661 C, T LRP2 chr2 170147501 170147502 C, G LRP2 chr2 170148744 170148745 A, G LRP2 chr2 170150670 170150671 A, G LRP2 chr2 170163767 170163768 C, T LRP2 chr2 170163815 170163816 G, T LRP2 chr2 170175333 170175334 C, T LRP2 chr2 170177381 170177382 A, G LRP2 chr2 170218815 170218816 C, T LRP2 chr2 170218846 170218847 C, G LRP2 chr2 173427052 173427053 G, T PDK1 chr2 173427079 173427080 A, G PDK1 chr2 173428873 173428874 C, T PDK1 chr2 178098678 178098679 C, T NFE2L2 chr2 178098721 178098722 A, G NFE2L2 chr2 187455277 187455278 C, T ITGAV chr2 187490231 187490232 A, G ITGAV chr2 187498106 187498107 C, T ITGAV chr2 187501741 187501742 A, G ITGAV chr2 187505701 187505702 A, T ITGAV chr2 187511465 187511466 A, G ITGAV chr2 187519337 187519338 G, T ITGAV chr2 187532009 187532010 G, T ITGAV chr2 187532372 187532373 G, T ITGAV chr2 187532416 187532417 A, G ITGAV chr2 187543373 187543374 C, T ITGAV chr2 190925076 190925077 C, T MSTN chr2 190927142 190927143 A, G MSTN chr2 190927159 190927160 C, T MSTN chr2 191899345 191899346 A, C STAT4 chr2 191905713 191905714 C, T STAT4 chr2 191922840 191922841 A, G STAT4 chr2 191927472 191927473 A, T STAT4 chr2 191996517 191996518 C, T STAT4 chr2 191996588 191996589 A, C STAT4 chr2 198257200 198257201 A, G SF3B1 chr2 198257794 198257795 C, T SF3B1 chr2 198257919 198257920 A, G SF3B1 chr2 198263721 198263722 A, G SF3B1 chr2 198265525 198265526 A, G SF3B1 chr2 198266660 198266661 C, T SF3B1 chr2 198266827 198266828 G, T SF3B1 chr2 198266861 198266862 A, T SF3B1 chr2 198270016 198270017 C, T SF3B1 chr2 198281458 198281459 A, T SF3B1 chr2 198281488 198281489 C, T SF3B1 chr2 198283304 198283305 C, T SF3B1 chr2 202122955 202122956 C, T CASP8 chr2 202134320 202134321 T CASP8 chr2 202141677 202141678 A, G CASP8 chr2 202149588 202149589 C, G CASP8 chr2 202149695 202149696 A, G CASP8 chr2 204732713 204732714 A, G CTLA4 chr2 204732739 204732740 C, G CTLA4 chr2 206562222 206562223 C, T NRP2 chr2 206562249 206562250 C, T NRP2 chr2 206562316 206562317 C, T NRP2 chr2 206565450 206565451 C, T NRP2 chr2 206581032 206581033 A, G NRP2 chr2 206588569 206588570 A, G NRP2 chr2 206590685 206590686 C, T NRP2 chr2 206592694 206592695 C, T NRP2 chr2 206605179 206605180 G, T NRP2 chr2 206605222 206605223 C, T NRP2 chr2 206605244 206605245 A, G NRP2 chr2 206608038 206608039 C, T NRP2 chr2 206610501 206610502 G, T NRP2 chr2 206630360 206630361 G NRP2 chr2 206631617 206631618 A, C NRP2 chr2 206656915 206656916 C, T NRP2 chr2 206656918 206656919 A, T NRP2 chr2 206659462 206659463 C, T NRP2 chr2 206659473 206659474 A, G NRP2 chr2 208631703 208631704 A, T FZD5 chr2 208631747 208631748 A, G FZD5 chr2 208631783 208631784 A, G FZD5 chr2 208632092 208632093 A, G FZD5 chr2 208632816 208632817 A, G FZD5 chr2 208633373 208633374 A, G FZD5 chr2 208633412 208633413 C, T FZD5 chr2 209106874 209106875 A, G IDH1 chr2 209108316 209108317 C, T IDH1 chr2 209113191 209113192 A, G IDH1 chr2 209113295 209113296 C, T IDH1 chr2 209113387 209113388 A, G IDH1 chr2 212251863 212251864 C, T ERBB4 chr2 212286681 212286682 C, G ERBB4 chr2 212488646 212488647 C, T ERBB4 chr2 212530216 212530217 C, T ERBB4 chr2 212537986 212537987 A, G ERBB4 chr2 212537993 212537994 A, T ERBB4 chr2 212543923 212543924 A, G ERBB4 chr2 212543929 212543930 A, G ERBB4 chr2 212615341 212615342 A, G ERBB4 chr2 215595068 215595069 G, T BARD1 chr2 215595202 215595203 A, G BARD1 chr2 215595644 215595645 C, T BARD1 chr2 215632255 215632256 A, G BARD1 chr2 215645463 215645464 C, G BARD1 chr2 215645977 215645978 T BARD1 chr2 215661882 215661883 G, T BARD1 chr2 215661910 215661911 A, C BARD1 chr2 215674089 215674090 G, T BARD1 chr2 215674223 215674224 A, G BARD1 chr2 219000192 219000193 A, G CXCR2 chr2 219000279 219000280 C, T CXCR2 chr2 219000459 219000460 C, T CXCR2 chr2 219028909 219028910 A, G CXCR1 chr2 219029301 219029302 G, T CXCR1 chr2 232320101 232320102 C, T NCL chr2 232320280 232320281 G NCL chr2 232320797 232320798 C, T NCL chr2 232321306 232321307 C, T NCL chr2 232321497 232321498 G, T NCL chr2 232322332 232322333 G, T NCL chr2 232323799 232323800 A, G NCL chr2 232323874 232323875 A, G NCL chr2 232325038 232325039 C, G NCL chr2 232325152 232325153 T NCL chr2 232325622 232325623 A, C NCL chr2 232326662 232326663 A, G NCL chr2 232326800 232326801 A, T NCL chr2 232327361 232327362 A, G NCL chr2 234590615 234590616 A, C UGT1A7 chr2 234590925 234590926 A, G UGT1A7 chr2 234591204 234591205 C, T UGT1A7 chr2 234599088 234599089 C, G UGT1A7 chr2 234669143 234669144 A, G UGT1A1 chr2 234669618 234669619 A, C UGT1A1 chr2 234675825 234675826 C, T UGT1A1 chr2 234675828 234675829 C, T UGT1A1 chr2 234676457 234676458 C, T UGT1A1 chr2 234835169 234835170 C, T TRPM8 chr2 234839403 234839404 C, T TRPM8 chr2 234854539 234854540 C, G TRPM8 chr2 234854546 234854547 A, T TRPM8 chr2 234854549 234854550 C, G TRPM8 chr2 234854551 234854552 A, G TRPM8 chr2 234856211 234856212 C, T TRPM8 chr2 234863787 234863788 A, G TRPM8 chr2 234878472 234878473 C, T TRPM8 chr2 234890618 234890619 A, T TRPM8 chr2 234891854 234891855 A, C TRPM8 chr2 234905077 234905078 C, T TRPM8 chr2 234915539 234915540 C, G TRPM8 chr2 234916793 234916794 A, G TRPM8 chr2 234916804 234916805 C, T TRPM8 chr2 234923123 234923124 A, C TRPM8 chr2 234926007 234926008 C, T TRPM8 chr2 242793272 242793273 A, G PDCD1 chr2 242793432 242793433 A, G PDCD1 chr2 242794812 242794813 C PDCD1 chr2 242800899 242800900 A, G PDCD1 chr3 10070335 10070336 C, G FANCD2 chr3 10070416 10070417 C, G FANCD2 chr3 10074645 10074646 C, G FANCD2 chr3 10076974 10076975 A, C FANCD2 chr3 10077954 10077955 A, G FANCD2 chr3 10080986 10080987 A, G FANCD2 chr3 10081410 10081411 A, G FANCD2 chr3 10081544 10081545 C, G FANCD2 chr3 10084395 10084396 A, G FANCD2 chr3 10085129 10085130 C, G FANCD2 chr3 10089688 10089689 G, T FANCD2 chr3 10089772 10089773 A, C FANCD2 chr3 10091034 10091035 C, T FANCD2 chr3 10094012 10094013 A, T FANCD2 chr3 10106514 10106515 C, T FANCD2 chr3 10108990 10108991 A, G FANCD2 chr3 10115042 10115043 C, T FANCD2 chr3 10119916 10119917 C, T FANCD2 chr3 10133948 10133949 A, G FANCD2 chr3 10136072 10136073 A, G FANCD2 chr3 10136102 10136103 C, T FANCD2 chr3 10138068 10138069 G, T FANCD2 chr3 10138188 10138189 C, T FANCD2 chr3 10142948 10142949 C, T FANCD2 chr3 12393124 12393125 C, G PPARG chr3 12413338 12413339 G, T PPARG chr3 12413589 12413590 A, G PPARG chr3 12434069 12434070 C, G PPARG chr3 12434090 12434091 A, C PPARG chr3 12458273 12458274 C, G PPARG chr3 12475556 12475557 C, T PPARG chr3 12626393 12626394 C, T RAF1 chr3 12626515 12626516 A, G RAF1 chr3 12629180 12629181 A, G RAF1 chr3 12645006 12645007 C, T RAF1 chr3 13539983 13539984 A, G HDAC11 chr3 13545696 13545697 C, T HDAC11 chr3 14188761 14188762 C, G XPC chr3 14189511 14189512 A, G XPC chr3 14190267 14190268 C, G XPC chr3 14193888 14193889 C, T XPC chr3 14199541 14199542 A, G XPC chr3 14199886 14199887 A, G XPC chr3 14199907 14199908 C, T XPC chr3 14200020 14200021 A, G XPC chr3 14201351 14201352 C, T XPC chr3 14207100 14207101 C, G XPC chr3 14212049 14212050 C, T XPC chr3 14220022 14220023 C, G XPC chr3 14220089 14220090 C, T XPC chr3 14220094 14220095 C, G XPC chr3 30686413 30686414 A, G TGFBR2 chr3 30713125 30713126 A, T TGFBR2 chr3 30713245 30713246 A, G TGFBR2 chr3 30713673 30713674 A, G TGFBR2 chr3 30713841 30713842 C, T TGFBR2 chr3 30715607 30715608 A, G TGFBR2 chr3 32995927 32995928 C, T CCR4 chr3 37042540 37042541 G, T MLH1 chr3 37048440 37048441 A, G MLH1 chr3 37050324 37050325 C, T MLH1 chr3 37050415 37050416 A MLH1 chr3 37053363 37053364 C, G MLH1 chr3 37053486 37053487 C, T MLH1 chr3 37053549 37053550 A, G MLH1 chr3 37053567 37053568 A, G MLH1 chr3 37067239 37067240 A, T MLH1 chr3 37083739 37083740 A, G MLH1 chr3 37092024 37092025 C, T MLH1 chr3 37107129 37107130 A, C MLH1 chr3 38180226 38180227 C, G MYD88 chr3 41266012 41266013 A, G CTNNB1 chr3 41266622 41266623 C, T CTNNB1 chr3 41275349 41275350 C, T CTNNB1 chr3 41275804 41275805 A, G CTNNB1 chr3 41280826 41280827 C, T CTNNB1 chr3 46414556 46414557 A, T CCR5 chr3 46415060 46415061 A, G CCR5 chr3 46415396 46415397 C, T CCR5 chr3 46480800 46480801 A, G LTF chr3 46480957 46480958 C, G LTF chr3 46482860 46482861 A, G LTF chr3 46482979 46482980 A, T LTF chr3 46484963 46484964 A, G LTF chr3 46488853 46488854 C, T LTF chr3 46488935 46488936 C, T LTF chr3 46490365 46490366 A, G LTF chr3 46490455 46490456 A, G LTF chr3 46495715 46495716 C, T LTF chr3 46496853 46496854 A, G LTF chr3 46497367 46497368 G, T LTF chr3 46497490 46497491 A, G LTF chr3 46501099 46501100 A, C LTF chr3 46501123 46501124 C, T LTF chr3 46501167 46501168 A, T LTF chr3 46501212 46501213 C, T LTF chr3 46501267 46501268 C, T LTF chr3 46509711 46509712 A, G LTF chr3 47098587 47098588 A, C SETD2 chr3 47103866 47103867 G, T SETD2 chr3 47108653 47108654 C, T SETD2 chr3 47125384 47125385 A, G SETD2 chr3 47144880 47144881 A, T SETD2 chr3 47161805 47161806 A, T SETD2 chr3 47162660 47162661 A, G SETD2 chr3 47162876 47162877 G, T SETD2 chr3 47162885 47162886 C, T SETD2 chr3 47163421 47163422 C, G SETD2 chr3 47163522 47163523 C, T SETD2 chr3 47163582 47163583 A, G SETD2 chr3 47165547 47165548 A, G SETD2 chr3 47165568 47165569 A, G SETD2 chr3 49924939 49924940 C, T MST1R chr3 49928034 49928035 A, G MST1R chr3 49928613 49928614 A, T MST1R chr3 49933239 49933240 A, G MST1R chr3 49933460 49933461 C, T MST1R chr3 49933615 49933616 C, T MST1R chr3 49935502 49935503 A, T MST1R chr3 49935525 49935526 G, T MST1R chr3 49936101 49936102 C, T MST1R chr3 49936607 49936608 C, T MST1R chr3 49940077 49940078 C, T MST1R chr3 49940498 49940499 A, G MST1R chr3 49940811 49940812 G, T MST1R chr3 52255919 52255920 C, T TLR9 chr3 52256696 52256697 C, T TLR9 chr3 52257890 52257891 G, T TLR9 chr3 52436258 52436259 C, G BAP1 chr3 52436266 52436267 C, T BAP1 chr3 52437205 52437206 A, G BAP1 chr3 52437257 52437258 C, T BAP1 chr3 52437747 52437748 A, C BAP1 chr3 52440268 52440269 C, T BAP1 chr3 52584714 52584715 A, G PBRM1 chr3 52584786 52584787 C, T PBRM1 chr3 52610650 52610651 A, T PBRM1 chr3 52620713 52620714 G, T PBRM1 chr3 52620744 52620745 A, G PBRM1 chr3 52643306 52643307 A, G PBRM1 chr3 52643684 52643685 C, T PBRM1 chr3 52658996 52658997 A, C PBRM1 chr3 52668637 52668638 A, G PBRM1 chr3 52668775 52668776 A, G PBRM1 chr3 52702505 52702506 C, T PBRM1 chr3 52712458 52712459 C, T PBRM1 chr3 69928509 69928510 A, G MITF chr3 69985837 69985838 A, G MITF chr3 70014383 70014384 A, G MITF chr3 70014386 70014387 A, G MITF chr3 70014446 70014447 C, T MITF chr3 89156883 89156884 C, G EPHA3 chr3 89456513 89456514 A, G EPHA3 chr3 89456554 89456555 A, T EPHA3 chr3 89480264 89480265 A, G EPHA3 chr3 89498427 89498428 A, G EPHA3 chr3 89521643 89521644 C, T EPHA3 chr3 89521692 89521693 C, T EPHA3 chr3 89521724 89521725 C, T EPHA3 chr3 96533682 96533683 C, T EPHA6 chr3 96533867 96533868 C, G EPHA6 chr3 96533873 96533874 C, T EPHA6 chr3 96963003 96963004 C, T EPHA6 chr3 97185265 97185266 G, T EPHA6 chr3 97194241 97194242 C, T EPHA6 chr3 97194316 97194317 G, T EPHA6 chr3 97202934 97202935 C, G EPHA6 chr3 97311482 97311483 C, T EPHA6 chr3 97331268 97331269 A, C EPHA6 chr3 97365073 97365074 A, G EPHA6 chr3 97365123 97365124 A, G EPHA6 chr3 119582290 119582291 A, G GSK3B chr3 119720979 119720980 A, T GSK3B chr3 124456741 124456742 C, G UMPS chr3 124458925 124458926 A, G UMPS chr3 124458937 124458938 A, T UMPS chr3 124462777 124462778 A, G UMPS chr3 124462807 124462808 C, T UMPS chr3 124462823 124462824 A, G UMPS chr3 124462958 124462959 A, G UMPS chr3 124483189 124483190 A, G ITGB5 chr3 124485234 124485235 A, G ITGB5 chr3 124492733 124492734 C, T ITGB5 chr3 124515307 124515308 A, G ITGB5 chr3 124515313 124515314 A, G ITGB5 chr3 124515394 124515395 A, G ITGB5 chr3 124515495 124515496 C, T ITGB5 chr3 124515508 124515509 A, G ITGB5 chr3 124515635 124515636 C, T ITGB5 chr3 124540192 124540193 A, G ITGB5 chr3 124605735 124605736 C, T ITGB5 chr3 124606473 124606474 A, G ITGB5 chr3 124606508 124606509 A, G ITGB5 chr3 124606535 124606536 C, T ITGB5 chr3 128200805 128200806 A, G GATA2 chr3 128204692 128204693 C, G GATA2 chr3 128204876 128204877 C, G GATA2 chr3 128204950 128204951 C, T GATA2 chr3 128205859 128205860 C, G GATA2 chr3 132050616 132050617 A, T ACPP chr3 132050623 132050624 A, G ACPP chr3 132063913 132063914 A, T ACPP chr3 132068830 132068831 C, T ACPP chr3 132068844 132068845 C, T ACPP chr3 132068875 132068876 A, G ACPP chr3 132068924 132068925 A, T ACPP chr3 132071536 132071537 A, C ACPP chr3 132071601 132071602 T ACPP chr3 132075706 132075707 A, G ACPP chr3 132075742 132075743 C, G ACPP chr3 132075745 132075746 A, G ACPP chr3 132075758 132075759 C, T ACPP chr3 134514578 134514579 C, T EPHB1 chr3 134644634 134644635 C, T EPHB1 chr3 134644635 134644636 G, T EPHB1 chr3 134670523 134670524 C, T EPHB1 chr3 134851604 134851605 C, T EPHB1 chr3 134851715 134851716 C, T EPHB1 chr3 134898741 134898742 C, T EPHB1 chr3 134920305 134920306 C, T EPHB1 chr3 134960158 134960159 C, G EPHB1 chr3 137743507 137743508 A, T CLDN18 chr3 138374238 138374239 G, T PIK3CB chr3 138384072 138384073 C, T PIK3CB chr3 138403666 138403667 C, T PIK3CB chr3 138413665 138413666 A, G PIK3CB chr3 138433567 138433568 C, T PIK3CB chr3 138456725 138456726 A, G PIK3CB chr3 138665028 138665029 C, G FOXL2 chr3 138665042 138665043 A, G FOXL2 chr3 138665063 138665064 A, G FOXL2 chr3 142168330 142168331 C, T ATR chr3 142178117 142178118 C, G ATR chr3 142178143 142178144 C, T ATR chr3 142188391 142188392 C, T ATR chr3 142217536 142217537 A, G ATR chr3 142217656 142217657 A, G ATR chr3 142222283 142222284 A, G ATR chr3 142231118 142231119 C, T ATR chr3 142242984 142242985 C, T ATR chr3 142272631 142272632 C, T ATR chr3 142272756 142272757 C, T ATR chr3 142277535 142277536 A, G ATR chr3 142277574 142277575 A, T ATR chr3 142280105 142280106 C, G ATR chr3 142281611 142281612 A, G ATR chr3 142286938 142286939 C, T ATR chr3 142287046 142287047 A, T ATR chr3 160118659 160118660 C, G SMC4 chr3 160119820 160119821 C, T SMC4 chr3 160120451 160120452 C, T SMC4 chr3 160130109 160130110 A, G SMC4 chr3 160132135 160132136 A, G SMC4 chr3 160143938 160143939 C, T SMC4 chr3 160143942 160143943 A, G SMC4 chr3 160144028 160144029 A, C SMC4 chr3 160144031 160144032 A, G SMC4 chr3 172224725 172224726 C, G TNFSF10 chr3 172232779 172232780 G, T TNFSF10 chr3 172241077 172241078 C, T TNFSF10 chr3 178921311 178921312 C, G PIK3CA chr3 178922272 178922273 A, C PIK3CA chr3 178922273 178922274 A, C PIK3CA chr3 178927409 178927410 A, G PIK3CA chr3 178938746 178938747 A, T PIK3CA chr3 178952019 178952020 C, T PIK3CA chr3 183210264 183210265 A, G KLHL6 chr3 183210293 183210294 C, T KLHL6 chr3 183211905 183211906 A, G KLHL6 chr3 183212025 183212026 C, T KLHL6 chr3 183217606 183217607 C, T KLHL6 chr3 183225809 183225810 C, T KLHL6 chr3 183226024 183226025 C, T KLHL6 chr3 183226071 183226072 A, G KLHL6 chr3 183226113 183226114 G, T KLHL6 chr3 183226185 183226186 C, T KLHL6 chr3 183226212 183226213 A, G KLHL6 chr3 185766561 185766562 A, G ETV5 chr3 185766565 185766566 C, T ETV5 chr3 185769791 185769792 G, T ETV5 chr3 185774812 185774813 A, C ETV5 chr3 185797810 185797811 C, G ETV5 chr3 187446210 187446211 C, T BCL6 chr3 187447031 187447032 A, G BCL6 chr3 187447700 187447701 A, C BCL6 chr3 189455680 189455681 C, T TP63 chr3 189587090 189587091 A, G TP63 chr3 189604148 189604149 G, T TP63 chr3 189604159 189604160 C, T TP63 chr3 189607099 189607100 A, C TP63 chr4 1801510 1801511 C, T FGFR3 chr4 1801541 1801542 A, G FGFR3 chr4 1803235 1803236 C, T FGFR3 chr4 1803250 1803251 C, T FGFR3 chr4 1803270 1803271 C, G FGFR3 chr4 1803306 1803307 C, T FGFR3 chr4 1803384 1803385 C, G FGFR3 chr4 1803703 1803704 C, T FGFR3 chr4 1805477 1805478 C, T FGFR3 chr4 1806039 1806040 C, T FGFR3 chr4 1806632 1806633 C, T FGFR3 chr4 1807410 1807411 A, G FGFR3 chr4 1807477 1807478 G, T FGFR3 chr4 1807710 1807711 C, T FGFR3 chr4 1807893 1807894 A, G FGFR3 chr4 1807921 1807922 A, G FGFR3 chr4 1809275 1809276 C, T FGFR3 chr4 1809348 1809349 A, G FGFR3 chr4 15835843 15835844 A, C CD38 chr4 15835982 15835983 C, T CD38 chr4 15839792 15839793 A, G CD38 chr4 15850109 15850110 A, G CD38 chr4 48139564 48139565 A, C TEC chr4 48147308 48147309 C, T TEC chr4 48148408 48148409 A, G TEC chr4 48148434 48148435 A, G TEC chr4 48152861 48152862 A, C TEC chr4 48152920 48152921 C, T TEC chr4 48165756 48165757 A, G TEC chr4 48165833 48165834 C, T TEC chr4 48169768 48169769 A, G TEC chr4 48169774 48169775 C, T TEC chr4 48170652 48170653 C, T TEC chr4 48170668 48170669 A, G TEC chr4 48172217 48172218 C, T TEC chr4 48172265 48172266 A, G TEC chr4 48173546 48173547 A, G TEC chr4 48178063 48178064 A, C TEC chr4 55124869 55124870 C, T PDGFRA chr4 55125057 55125058 A, T PDGFRA chr4 55129830 55129831 C, T PDGFRA chr4 55130077 55130078 C, T PDGFRA chr4 55133714 55133715 A, G PDGFRA chr4 55133725 55133726 G, T PDGFRA chr4 55133805 55133806 A, G PDGFRA chr4 55138642 55138643 A, G PDGFRA chr4 55139770 55139771 C, T PDGFRA chr4 55141054 55141055 A, G PDGFRA chr4 55143576 55143577 A, G PDGFRA chr4 55145112 55145113 A, G PDGFRA chr4 55151507 55151508 G, T PDGFRA chr4 55151508 55151509 C, T PDGFRA chr4 55151710 55151711 A, C PDGFRA chr4 55152039 55152040 C, T PDGFRA chr4 55161253 55161254 C, T PDGFRA chr4 55524303 55524304 C, T KIT chr4 55561861 55561862 G, T KIT chr4 55564643 55564644 G KIT chr4 55575592 55575593 C, T KIT chr4 55597457 55597458 A, G KIT chr4 55599267 55599268 C, T KIT chr4 55602764 55602765 C, G KIT chr4 55604638 55604639 C, T KIT chr4 55946170 55946171 A, G KDR chr4 55956224 55956225 C, T KDR chr4 55961158 55961159 C, T KDR chr4 55961872 55961873 C, T KDR chr4 55964834 55964835 C, T KDR chr4 55968052 55968053 A, C KDR chr4 55970781 55970782 A, G KDR chr4 55970962 55970963 A, G KDR chr4 55972973 55972974 A, T KDR chr4 55973931 55973932 A, C KDR chr4 55979557 55979558 C, T KDR chr4 55987392 55987393 C, G KDR chr4 55991460 55991461 A, C KDR chr4 66197803 66197804 C, T EPHA5 chr4 66201633 66201634 A, G EPHA5 chr4 66217077 66217078 A, G EPHA5 chr4 66218755 66218756 C, T EPHA5 chr4 66230726 66230727 A, T EPHA5 chr4 66231698 66231699 A, G EPHA5 chr4 66242660 66242661 A, G EPHA5 chr4 66280106 66280107 C, G EPHA5 chr4 66286313 66286314 G EPHA5 chr4 66467731 66467732 A, G EPHA5 chr4 66509039 66509040 G, T EPHA5 chr4 66509084 66509085 G, T EPHA5 chr4 66535283 66535284 A, G EPHA5 chr4 68619909 68619910 C, G GNRHR chr4 74302799 74302800 A, C AFP chr4 74302869 74302870 C, T AFP chr4 74309178 74309179 C AFP chr4 74310843 74310844 A, G AFP chr4 74316376 74316377 A, G AFP chr4 74318176 74318177 C, T AFP chr4 74319537 74319538 C, G AFP chr4 84222207 84222208 A, G HPSE chr4 84223454 84223455 A, G HPSE chr4 84223460 84223461 C, G HPSE chr4 84230032 84230033 C, T HPSE chr4 84230618 84230619 C, T HPSE chr4 84234228 84234229 A, G HPSE chr4 84240460 84240461 G, T HPSE chr4 84240653 84240654 A, G HPSE chr4 84243548 84243549 A, G HPSE chr4 88898940 88898941 C, T SPP1 chr4 88902691 88902692 C, T SPP1 chr4 88902724 88902725 A, G SPP1 chr4 88902850 88902851 C, T SPP1 chr4 88903773 88903774 A, G SPP1 chr4 88903852 88903853 C, T SPP1 chr4 88904004 88904005 A, G SPP1 chr4 89018564 89018565 A, G ABCG2 chr4 89020426 89020427 A, C ABCG2 chr4 89020437 89020438 C, T ABCG2 chr4 89028283 89028284 A, G ABCG2 chr4 89034550 89034551 C, T ABCG2 chr4 89039242 89039243 C, T ABCG2 chr4 89052322 89052323 G, T ABCG2 chr4 89053717 89053718 C, T ABCG2 chr4 89053789 89053790 A, G ABCG2 chr4 89060908 89060909 C, T ABCG2 chr4 89080350 89080351 C, G ABCG2 chr4 89080400 89080401 G, T ABCG2 chr4 89080413 89080414 G, T ABCG2 chr4 103446730 103446731 C NFKB1 chr4 103446736 103446737 A, T NFKB1 chr4 103514657 103514658 C, T NFKB1 chr4 103514736 103514737 C, T NFKB1 chr4 103514740 103514741 C, T NFKB1 chr4 103518699 103518700 A, G NFKB1 chr4 103518840 103518841 A, T NFKB1 chr4 103528816 103528817 G, T NFKB1 chr4 103533630 103533631 C, G NFKB1 chr4 103534559 103534560 C, G NFKB1 chr4 103534577 103534578 A, G NFKB1 chr4 104027497 104027498 G, T CENPE chr4 104030206 104030207 C, T CENPE chr4 104059440 104059441 C, T CENPE chr4 104059449 104059450 C, T CENPE chr4 104059541 104059542 A, G CENPE chr4 104061550 104061551 G, T CENPE chr4 104061992 104061993 C, G CENPE chr4 104063070 104063071 C, T CENPE chr4 104066322 104066323 G, T CENPE chr4 104066347 104066348 A, G CENPE chr4 104066460 104066461 A, G CENPE chr4 104067126 104067127 A, G CENPE chr4 104067194 104067195 C, T CENPE chr4 104068552 104068553 A, T CENPE chr4 104070040 104070041 A, G CENPE chr4 104070432 104070433 A, T CENPE chr4 104079423 104079424 C, T CENPE chr4 104080216 104080217 A, C CENPE chr4 104081919 104081920 C, T CENPE chr4 104082348 104082349 C, T CENPE chr4 104096062 104096063 A, G CENPE chr4 104102562 104102563 C, T CENPE chr4 104104005 104104006 A, G CENPE chr4 104107042 104107043 C, T CENPE chr4 104107057 104107058 G, T CENPE chr4 104115716 104115717 A, G CENPE chr4 104116431 104116432 A, G CENPE chr4 104117190 104117191 A, G CENPE chr4 104117218 104117219 C, T CENPE chr4 104117303 104117304 C, T CENPE chr4 104118026 104118027 G, T CENPE chr4 106111580 106111581 A, G TET2 chr4 106155184 106155185 C, G TET2 chr4 106155704 106155705 C, T TET2 chr4 106155750 106155751 A, G TET2 chr4 106156162 106156163 A, G TET2 chr4 106156186 106156187 C, T TET2 chr4 106156982 106156983 A, G TET2 chr4 106158188 106158189 A, G TET2 chr4 106158214 106158215 C, T TET2 chr4 106158215 106158216 A, G TET2 chr4 106190731 106190732 A, C TET2 chr4 106196950 106196951 A, G TET2 chr4 106196999 106197000 A, G TET2 chr4 110638809 110638810 C, T PLA2G12A chr4 123377481 123377482 A, C IL2 chr4 123747941 123747942 C, G FGF2 chr4 123747946 123747947 A, G FGF2 chr4 123748085 123748086 C, T FGF2 chr4 123748523 123748524 C, T FGF2 chr4 123797427 123797428 G, T FGF2 chr4 128802344 128802345 A, G PLK4 chr4 128814491 128814492 A, G PLK4 chr4 128819617 128819618 A, G PLK4 chr4 139104413 139104414 C, T SLC7A11 chr4 139104414 139104415 C, T SLC7A11 chr4 139106248 139106249 C, T SLC7A11 chr4 139135798 139135799 C, T SLC7A11 chr4 139140387 139140388 A, G SLC7A11 chr4 139140493 139140494 C, G SLC7A11 chr4 139153505 139153506 G, T SLC7A11 chr4 139153538 139153539 A, T SLC7A11 chr4 148441138 148441139 A, G EDNRA chr4 148461036 148461037 C, T EDNRA chr4 148461072 148461073 A, G EDNRA chr4 153303353 153303354 A, C FBXW7 chr4 153332558 153332559 C, T FBXW7 chr4 154624655 154624656 C, T TLR2 chr4 154625408 154625409 C, T TLR2 chr4 154626401 154626402 A, G TLR2 chr4 177605222 177605223 A, G VEGFC chr4 177608706 177608707 C, T VEGFC chr4 177649119 177649120 C, T VEGFC chr4 177713287 177713288 A, G VEGFC chr4 185552134 185552135 C, T CASP3 chr4 185553097 185553098 G, T CASP3 chr4 185556617 185556618 C, T CASP3 chr4 185559486 185559487 C, G CASP3 chr4 185565619 185565620 G, T CASP3 chr4 185565620 185565621 C, T CASP3 chr4 187003677 187003678 A, G TLR3 chr4 187003758 187003759 G, T TLR3 chr4 187004073 187004074 C, T TLR3 chr4 187004516 187004517 A, G TLR3 chr4 187004543 187004544 C, T TLR3 chr4 187004766 187004767 A, C TLR3 chr4 187005048 187005049 A, T TLR3 chr4 187005864 187005865 C, T TLR3 chr4 187005867 187005868 G, T TLR3 chr5 1254450 1254451 C, T TERT chr5 1255519 1255520 A, G TERT chr5 1268579 1268580 C, T TERT chr5 1279504 1279505 A, G TERT chr5 1279626 1279627 A, G TERT chr5 1280251 1280252 A, G TERT chr5 1282653 1282654 A, G TERT chr5 1294085 1294086 C, T TERT chr5 1294165 1294166 C, T TERT chr5 35068247 35068248 C, G PRLR chr5 35072711 35072712 G, T PRLR chr5 35084646 35084647 C, T PRLR chr5 35089576 35089577 A, G PRLR chr5 35857176 35857177 C, G IL7R chr5 35857206 35857207 C, T IL7R chr5 35857234 35857235 C, G IL7R chr5 35861023 35861024 A, G IL7R chr5 35861067 35861068 C, T IL7R chr5 35871189 35871190 A, G IL7R chr5 35871272 35871273 C, T IL7R chr5 35873567 35873568 A, C IL7R chr5 35873604 35873605 A, G IL7R chr5 35874574 35874575 C, T IL7R chr5 35875592 35875593 A, T IL7R chr5 35876273 35876274 A, G IL7R chr5 35876438 35876439 A, G IL7R chr5 35876448 35876449 C, T IL7R chr5 38942448 38942449 A, G RICTOR chr5 38950775 38950776 A, G RICTOR chr5 38954993 38954994 C, T RICTOR chr5 38955795 38955796 A, G RICTOR chr5 38958876 38958877 C, T RICTOR chr5 38959419 38959420 A, G RICTOR chr5 38962542 38962543 A, G RICTOR chr5 38967376 38967377 C, T RICTOR chr5 44305091 44305092 A, T FGF10 chr5 44305132 44305133 A, G FGF10 chr5 44388816 44388817 C, T FGF10 chr5 50040669 50040670 C PARP8 chr5 50045966 50045967 G, T PARP8 chr5 50057728 50057729 A, G, T PARP8 chr5 50074530 50074531 A, G PARP8 chr5 50091151 50091152 A, G PARP8 chr5 50091161 50091162 A, G PARP8 chr5 50091169 50091170 C, T PARP8 chr5 50118249 50118250 A, G PARP8 chr5 50122644 50122645 G, T PARP8 chr5 50128569 50128570 A, T PARP8 chr5 50129160 50129161 C, T PARP8 chr5 52084299 52084300 A, G ITGA1 chr5 52157373 52157374 C, T ITGA1 chr5 52177742 52177743 A, G ITGA1 chr5 52193286 52193287 C, T ITGA1 chr5 52193390 52193391 C, T ITGA1 chr5 52201721 52201722 C, T ITGA1 chr5 52201744 52201745 C, T ITGA1 chr5 52214580 52214581 A, G ITGA1 chr5 52216216 52216217 C, T ITGA1 chr5 52218693 52218694 C, T ITGA1 chr5 52223349 52223350 A, G ITGA1 chr5 52228024 52228025 A, G ITGA1 chr5 52229744 52229745 G, T ITGA1 chr5 52235644 52235645 C, T ITGA1 chr5 52235801 52235802 G, T ITGA1 chr5 52240809 52240810 A, G ITGA1 chr5 56111444 56111445 A, G MAP3K1 chr5 56111480 56111481 C, T MAP3K1 chr5 56111564 56111565 A, G MAP3K1 chr5 56111750 56111751 C, G MAP3K1 chr5 56161786 56161787 A, G MAP3K1 chr5 56168789 56168790 A, G MAP3K1 chr5 56171088 56171089 A, G MAP3K1 chr5 56177442 56177443 A, G MAP3K1 chr5 56177742 56177743 A, G MAP3K1 chr5 56178216 56178217 A, C MAP3K1 chr5 56179340 56179341 A, G MAP3K1 chr5 67522721 67522722 C, T PIK3R1 chr5 67535721 67535722 C, T PIK3R1 chr5 67535788 67535789 C, T PIK3R1 chr5 67535809 67535810 A, C PIK3R1 chr5 67575547 67575548 C, T PIK3R1 chr5 67588147 67588148 A, G PIK3R1 chr5 67589037 67589038 A, G PIK3R1 chr5 67593362 67593363 C, T PIK3R1 chr5 68530702 68530703 A, G CDK7 chr5 68531252 68531253 C, T CDK7 chr5 79950402 79950403 C, T DHFR chr5 79950496 79950497 C, T MSH3 chr5 79950507 79950508 C, T MSH3 chr5 79950511 79950512 A, G MSH3 chr5 79950716 79950717 C, T MSH3 chr5 79950723 79950724 C, G MSH3 chr5 79950726 79950727 C, G MSH3 chr5 79952389 79952390 C, T MSH3 chr5 79960954 79960955 A, G MSH3 chr5 79966028 79966029 A, G MSH3 chr5 79968257 79968258 A, T MSH3 chr5 79968270 79968271 A, G MSH3 chr5 80024782 80024783 A, G MSH3 chr5 80149980 80149981 A, G MSH3 chr5 112043383 112043384 G, T APC chr5 112043491 112043492 A, C APC chr5 112111309 112111310 A, T APC chr5 112116631 112116632 C, T APC chr5 112136946 112136947 A, T APC chr5 112162853 112162854 C, T APC chr5 112164560 112164561 A, G APC chr5 112164620 112164621 A, G APC chr5 112173898 112173899 C, T APC chr5 112175022 112175023 A, G APC chr5 112175769 112175770 A, G APC chr5 112176324 112176325 A, G APC chr5 112176558 112176559 G, T APC chr5 112176755 112176756 A, T APC chr5 112177170 112177171 A, G APC chr5 112178994 112178995 A, G APC chr5 112198127 112198128 C, T APC chr5 131409581 131409582 A, G CSF2 chr5 131409596 131409597 A, G CSF2 chr5 131411459 131411460 C, T CSF2 chr5 131994030 131994031 A, C IL13 chr5 131995078 131995079 C, T IL13 chr5 131995963 131995964 A, G IL13 chr5 132009709 132009710 C, T IL4 chr5 132009786 132009787 A, G IL4 chr5 132018131 132018132 A, G IL4 chr5 132018168 132018169 A, C IL4 chr5 138117937 138117938 A, G CTNNA1 chr5 138147948 138147949 G, T CTNNA1 chr5 138148035 138148036 A, G CTNNA1 chr5 138221988 138221989 C, G CTNNA1 chr5 138266545 138266546 A, G CTNNA1 chr5 138268310 138268311 A, G CTNNA1 chr5 139722344 139722345 A, G HBEGF chr5 139725960 139725961 A, G HBEGF chr5 141975066 141975067 A, C FGF1 chr5 149433856 149433857 C, G CSF1R chr5 149435607 149435608 C, G CSF1R chr5 149435758 149435759 A, G CSF1R chr5 149439257 149439258 A, G CSF1R chr5 149447765 149447766 A, G CSF1R chr5 149447770 149447771 A, G CSF1R chr5 149450131 149450132 C, T CSF1R chr5 149456810 149456811 A, G CSF1R chr5 149456892 149456893 C, T CSF1R chr5 149456994 149456995 A, C CSF1R chr5 149457677 149457678 A, G CSF1R chr5 149457682 149457683 C, T CSF1R chr5 149459789 149459790 C CSF1R chr5 149460342 149460343 A, G CSF1R chr5 149460444 149460445 A, G CSF1R chr5 149460552 149460553 A, G CSF1R chr5 149465862 149465863 A, G CSF1R chr5 149465890 149465891 C, T CSF1R chr5 149495394 149495395 C, T PDGFRB chr5 149495536 149495537 A, G PDGFRB chr5 149497176 149497177 C, T PDGFRB chr5 149497198 149497199 A, C PDGFRB chr5 149497227 149497228 A, G PDGFRB chr5 149499671 149499672 C, T PDGFRB chr5 149499725 149499726 A, T PDGFRB chr5 149500401 149500402 C, T PDGFRB chr5 149504257 149504258 C, T PDGFRB chr5 149505053 149505054 C, T PDGFRB chr5 149509445 149509446 C, T PDGFRB chr5 149509507 149509508 A, G PDGFRB chr5 149510045 149510046 A, C PDGFRB chr5 149513402 149513403 C, T PDGFRB chr5 149515379 149515380 A, G PDGFRB chr5 149515396 149515397 A, T PDGFRB chr5 149781564 149781565 C, T CD74 chr5 149781626 149781627 C, T CD74 chr5 149781994 149781995 A, G CD74 chr5 149785923 149785924 C, T CD74 chr5 149785933 149785934 C, G CD74 chr5 149792336 149792337 C, T CD74 chr5 156607956 156607957 A, C ITK chr5 156636026 156636027 G, T ITK chr5 156644938 156644939 A, G ITK chr5 156649816 156649817 A, G ITK chr5 156665280 156665281 C, T ITK chr5 156670822 156670823 A, G ITK chr5 156675843 156675844 C, T ITK chr5 156679572 156679573 A, G ITK chr5 156679575 156679576 C, T ITK chr5 162866547 162866548 C, T CCNG1 chr5 162870635 162870636 C, G CCNG1 chr5 162870725 162870726 C, G CCNG1 chr5 170819886 170819887 A, G NPM1 chr5 170837456 170837457 A, G NPM1 chr5 175110280 175110281 C, T HRH2 chr5 175110778 175110779 A, G HRH2 chr5 175112619 175112620 C, T HRH2 chr5 176516541 176516542 C, T FGFR4 chr5 176516630 176516631 A, G FGFR4 chr5 176516952 176516953 A, G FGFR4 chr5 176516953 176516954 C, T FGFR4 chr5 176517291 176517292 A, G FGFR4 chr5 176517325 176517326 C, T FGFR4 chr5 176517460 176517461 G, T FGFR4 chr5 176517796 176517797 C, T FGFR4 chr5 176518036 176518037 A, G FGFR4 chr5 176518765 176518766 C, T FGFR4 chr5 176518783 176518784 C, T FGFR4 chr5 176519515 176519516 A, G FGFR4 chr5 176520242 176520243 A, G FGFR4 chr5 176522561 176522562 C, T FGFR4 chr5 176523185 176523186 A, G FGFR4 chr5 176523561 176523562 A, C FGFR4 chr5 176523596 176523597 A, G FGFR4 chr5 176524702 176524703 A, T FGFR4 chr5 180030324 180030325 C, T FLT4 chr5 180035993 180035994 A, G FLT4 chr5 180039605 180039606 C, T FLT4 chr5 180039638 180039639 A, G FLT4 chr5 180043387 180043388 A, G FLT4 chr5 180043438 180043439 A, G FLT4 chr5 180046343 180046344 C, G FLT4 chr5 180046635 180046636 C, G FLT4 chr5 180048034 180048035 C, T FLT4 chr5 180049807 180049808 C, T FLT4 chr5 180051002 180051003 C, T FLT4 chr5 180052945 180052946 A, G FLT4 chr5 180053089 180053090 A, G FLT4 chr5 180053096 180053097 C, T FLT4 chr5 180056043 180056044 A, G FLT4 chr5 180056862 180056863 C, T FLT4 chr5 180056985 180056986 C, T FLT4 chr5 180057230 180057231 A, C FLT4 chr5 180057248 180057249 A, G FLT4 chr5 180057292 180057293 C, T FLT4 chr5 180058760 180058761 A, C FLT4 chr5 180076459 180076460 C, G FLT4 chr6 393358 393359 C, G IRF4 chr6 395888 395889 A, G IRF4 chr6 398774 398775 A, G IRF4 chr6 405145 405146 C, G IRF4 chr6 18130992 18130993 C, T TPMT chr6 18134020 18134021 A, C TPMT chr6 18134077 18134078 A, C TPMT chr6 18139227 18139228 C, T TPMT chr6 18139801 18139802 A, T TPMT chr6 26087778 26087779 G HFE chr6 26091178 26091179 C, G HFE chr6 26091335 26091336 C, T HFE chr6 26092864 26092865 C, G HFE chr6 26094366 26094367 A, G HFE chr6 26094432 26094433 C, T HFE chr6 26094514 26094515 C, T HFE chr6 26096747 26096748 C, G HFE chr6 31540555 31540556 C, T LTA chr6 31540756 31540757 A, C LTA chr6 31543604 31543605 G, T TNF chr6 33288074 33288075 A, C DAXX chr6 33288270 33288271 A, G DAXX chr6 33288505 33288506 A, C DAXX chr6 35391786 35391787 C, T PPARD chr6 35420266 35420267 C, T FANCE chr6 35423661 35423662 A, C FANCE chr6 35423885 35423886 C, T FANCE chr6 35425415 35425416 A, G FANCE chr6 35426131 35426132 A, G FANCE chr6 35426174 35426175 C, T FANCE chr6 35430685 35430686 A, G FANCE chr6 37138304 37138305 G PIM1 chr6 37138443 37138444 C, T PIM1 chr6 37139321 37139322 C, T PIM1 chr6 37141695 37141696 C PIM1 chr6 41533572 41533573 A, G FOXP4 chr6 41533578 41533579 A, C FOXP4 chr6 41554992 41554993 C, G FOXP4 chr6 41555211 41555212 C, T FOXP4 chr6 41557566 41557567 C, T FOXP4 chr6 41557646 41557647 A, C FOXP4 chr6 41557944 41557945 A, G FOXP4 chr6 41558042 41558043 C, T FOXP4 chr6 41558951 41558952 C, T FOXP4 chr6 41565471 41565472 C, T FOXP4 chr6 41565580 41565581 C, T FOXP4 chr6 41566508 41566509 A, G FOXP4 chr6 41903781 41903782 A, C CCND3 chr6 41903782 41903783 A, G CCND3 chr6 41904482 41904483 C, T CCND3 chr6 41904955 41904956 A, G CCND3 chr6 44187385 44187386 C, T SLC29A1 chr6 44197801 44197802 A, G SLC29A1 chr6 44198311 44198312 A, G SLC29A1 chr6 44199201 44199202 C, T SLC29A1 chr6 44217373 44217374 G, T HSP90AB1 chr6 44219098 44219099 G, T HSP90AB1 chr6 44219709 44219710 A, C HSP90AB1 chr6 44219925 44219926 A, G HSP90AB1 chr6 44221068 44221069 C HSP90AB1 chr6 44221141 44221142 C, T HSP90AB1 chr6 44221166 44221167 G, T HSP90AB1 chr6 74405948 74405949 C, G CD109 chr6 74405973 74405974 C, G CD109 chr6 74407181 74407182 G, T CD109 chr6 74432922 74432923 C, T CD109 chr6 74440271 74440272 A, C CD109 chr6 74466376 74466377 C, T CD109 chr6 74491001 74491002 G, T CD109 chr6 74493431 74493432 A, C CD109 chr6 74493597 74493598 A, G CD109 chr6 74495202 74495203 A, G CD109 chr6 74495256 74495257 A, G CD109 chr6 74496993 74496994 G, T CD109 chr6 74497008 74497009 A, G CD109 chr6 74497101 74497102 A, G CD109 chr6 74497151 74497152 A, G CD109 chr6 74513053 74513054 A, G CD109 chr6 74517983 74517984 A, G CD109 chr6 74519701 74519702 G, T CD109 chr6 74520862 74520863 C, T CD109 chr6 74521946 74521947 C, T CD109 chr6 74521947 74521948 G, T CD109 chr6 74521998 74521999 A, T CD109 chr6 74524723 74524724 A, G CD109 chr6 74524756 74524757 G, T CD109 chr6 74530289 74530290 A, G CD109 chr6 74533191 74533192 G, T CD109 chr6 93967850 93967851 C, T EPHA7 chr6 93982099 93982100 C, T EPHA7 chr6 93982123 93982124 A, G EPHA7 chr6 94067980 94067981 C, T EPHA7 chr6 94120218 94120219 A, G EPHA7 chr6 94120638 94120639 C, T EPHA7 chr6 94124352 94124353 A, C EPHA7 chr6 94124529 94124530 A, C EPHA7 chr6 106547371 106547372 C, G PRDM1 chr6 106552891 106552892 C, G PRDM1 chr6 106555024 106555025 A, G PRDM1 chr6 106555194 106555195 A, G PRDM1 chr6 111995665 111995666 A, G FYN chr6 112015558 112015559 C, T FYN chr6 112015740 112015741 C, T FYN chr6 112015822 112015823 G, T FYN chr6 112375643 112375644 A, G WISP3 chr6 112381262 112381263 C, T WISP3 chr6 112382222 112382223 A, T WISP3 chr6 112382312 112382313 G, T WISP3 chr6 112382322 112382323 C, T WISP3 chr6 112382381 112382382 C, T WISP3 chr6 112388226 112388227 A, G WISP3 chr6 112390564 112390565 A, G WISP3 chr6 112390649 112390650 A, C WISP3 chr6 114265586 114265587 C, T HDAC2 chr6 114279976 114279977 C, T HDAC2 chr6 114281188 114281189 C, T HDAC2 chr6 114281235 114281236 C, T HDAC2 chr6 114292184 114292185 C, T HDAC2 chr6 114292361 114292362 C, G HDAC2 chr6 117622183 117622184 C, G ROS1 chr6 117622187 117622188 G, T ROS1 chr6 117622232 117622233 C, T ROS1 chr6 117632150 117632151 A, G ROS1 chr6 117638254 117638255 G, T ROS1 chr6 117639300 117639301 C, T ROS1 chr6 117639418 117639419 C, T ROS1 chr6 117642456 117642457 A, G ROS1 chr6 117645661 117645662 C, T ROS1 chr6 117650531 117650532 C, G ROS1 chr6 117665327 117665328 G, T ROS1 chr6 117678082 117678083 A, G ROS1 chr6 117681088 117681089 C, T ROS1 chr6 117683820 117683821 A, G ROS1 chr6 117686839 117686840 C, T ROS1 chr6 117704606 117704607 C, T ROS1 chr6 117710572 117710573 C, G ROS1 chr6 117710660 117710661 C, T ROS1 chr6 117714345 117714346 C, G ROS1 chr6 117717347 117717348 C, T ROS1 chr6 117718217 117718218 A, G ROS1 chr6 117718302 117718303 A, G ROS1 chr6 117724378 117724379 C, T ROS1 chr6 117724461 117724462 A, C ROS1 chr6 117725577 117725578 A, T ROS1 chr6 117730818 117730819 A, G ROS1 chr6 117730898 117730899 G, T ROS1 chr6 138196065 138196066 G, T TNFAIP3 chr6 138196816 138196817 C, G TNFAIP3 chr6 138197328 138197329 C, T TNFAIP3 chr6 138197330 138197331 A, C TNFAIP3 chr6 138202377 138202378 C, T TNFAIP3 chr6 152129275 152129276 A, G ESR1 chr6 152129307 152129308 C, G ESR1 chr6 152130313 152130314 C, T ESR1 chr6 152201874 152201875 C, T ESR1 chr6 152265521 152265522 C, G ESR1 chr6 152419986 152419987 A, G ESR1 chr6 152446315 152446316 C, T ESR1 chr6 152446319 152446320 C, T ESR1 chr6 152446486 152446487 C, T ESR1 chr6 160106087 160106088 A, C SOD2 chr6 160113598 160113599 G, T SOD2 chr6 160113871 160113872 A, G SOD2 chr6 160114167 160114168 C, T SOD2 chr6 160114260 160114261 C, G SOD2 chr6 160430209 160430210 A, T IGF2R chr6 160448263 160448264 A, G IGF2R chr6 160448314 160448315 C, T IGF2R chr6 160448323 160448324 C, G IGF2R chr6 160453560 160453561 G, T IGF2R chr6 160453568 160453569 A, G IGF2R chr6 160464288 160464289 A, G IGF2R chr6 160468179 160468180 A, G IGF2R chr6 160468277 160468278 A, G IGF2R chr6 160468308 160468309 A, G IGF2R chr6 160469541 160469542 A, G IGF2R chr6 160479881 160479882 A, G IGF2R chr6 160479923 160479924 C, T IGF2R chr6 160482591 160482592 C, T IGF2R chr6 160482928 160482929 C, G IGF2R chr6 160483732 160483733 A, G IGF2R chr6 160485495 160485496 A, G IGF2R chr6 160493833 160493834 A, G IGF2R chr6 160494408 160494409 A, G IGF2R chr6 160499212 160499213 C, T IGF2R chr6 160499380 160499381 C, T IGF2R chr6 160500811 160500812 C, T IGF2R chr6 160510101 160510102 A, G IGF2R chr6 160524772 160524773 A, T IGF2R chr6 160524810 160524811 C, T IGF2R chr6 160524824 160524825 A, G IGF2R chr6 160524875 160524876 A, G IGF2R chr6 160953641 160953642 A, G LPA chr6 160961136 160961137 C, T LPA chr6 160962234 160962235 A, G LPA chr6 160969628 160969629 A, G LPA chr6 160969737 160969738 C, G LPA chr6 161007495 161007496 C, G LPA chr6 161007537 161007538 C, G LPA chr6 161010765 161010766 A, T LPA chr6 161015171 161015172 A, C LPA chr6 161016373 161016374 C, T LPA chr6 161022168 161022169 C, T LPA chr6 161026196 161026197 A, G LPA chr6 166571934 166571935 C, T T chr6 166572004 166572005 C, T T chr6 166572011 166572012 C, T T chr6 166574307 166574308 C, T T chr6 166574461 166574462 A, G T chr6 166579269 166579270 C, T T chr6 166580187 166580188 A, G T chr6 166580256 166580257 A, G T chr7 2946337 2946338 A, G CARD11 chr7 2951823 2951824 A, G CARD11 chr7 2954961 2954962 A, G CARD11 chr7 2956917 2956918 A, C CARD11 chr7 2957004 2957005 C, T CARD11 chr7 2959171 2959172 A, G CARD11 chr7 2962292 2962293 C, G CARD11 chr7 2962418 2962419 C, T CARD11 chr7 2963838 2963839 A, G CARD11 chr7 2963883 2963884 C, T CARD11 chr7 2966333 2966334 A, G CARD11 chr7 2966444 2966445 G, T CARD11 chr7 2966473 2966474 C, G CARD11 chr7 2968244 2968245 C, T CARD11 chr7 2968290 2968291 A, G CARD11 chr7 2968354 2968355 A, G CARD11 chr7 2968358 2968359 C, T CARD11 chr7 2969679 2969680 A, G CARD11 chr7 2969688 2969689 G, T CARD11 chr7 2974164 2974165 C, T CARD11 chr7 2976751 2976752 C, T CARD11 chr7 2976766 2976767 A, G CARD11 chr7 2976799 2976800 C, T CARD11 chr7 2985585 2985586 C, G CARD11 chr7 13950837 13950838 C, T ETV1 chr7 13971422 13971423 C, T ETV1 chr7 13975299 13975300 A, G ETV1 chr7 13978808 13978809 C, T ETV1 chr7 14017006 14017007 C, T ETV1 chr7 14017007 14017008 C, G ETV1 chr7 14025726 14025727 C, T ETV1 chr7 14025765 14025766 A, T ETV1 chr7 50367291 50367292 A, C IKZF1 chr7 50435776 50435777 G, T IKZF1 chr7 50435902 50435903 A, C IKZF1 chr7 50436032 50436033 A, G IKZF1 chr7 50467766 50467767 A, C IKZF1 chr7 50467773 50467774 A, G IKZF1 chr7 50467940 50467941 C, T IKZF1 chr7 55214347 55214348 C, T EGFR chr7 55214404 55214405 A, G EGFR chr7 55214442 55214443 A, G EGFR chr7 55218902 55218903 C, T EGFR chr7 55227824 55227825 A, G EGFR chr7 55227849 55227850 A, G EGFR chr7 55229254 55229255 A, G EGFR chr7 55231425 55231426 C, T EGFR chr7 55233037 55233038 A, G EGFR chr7 55233088 55233089 C, T EGFR chr7 55236256 55236257 A, C EGFR chr7 55237976 55237977 C, T EGFR chr7 55238036 55238037 A, C EGFR chr7 55238086 55238087 C, T EGFR chr7 55238873 55238874 A, T EGFR chr7 55241754 55241755 A, G EGFR chr7 55249062 55249063 A, G EGFR chr7 55260439 55260440 C, T EGFR chr7 55268896 55268897 A, C EGFR chr7 55268915 55268916 C, T EGFR chr7 65425893 65425894 A, G GUSB chr7 81346684 81346685 C, T HGF chr7 81359050 81359051 C, T HGF chr7 81372323 81372324 C, G HGF chr7 81374350 81374351 A, G HGF chr7 81386482 81386483 C, T HGF chr7 81388041 81388042 C, T HGF chr7 86394592 86394593 A, G GRM3 chr7 86415986 86415987 C, T GRM3 chr7 86468515 86468516 C, T GRM3 chr7 87133537 87133538 A, G ABCB1 chr7 87133803 87133804 A, C ABCB1 chr7 87138644 87138645 A, G ABCB1 chr7 87138658 87138659 A, T ABCB1 chr7 87145808 87145809 A, G ABCB1 chr7 87160617 87160618 A, C, T ABCB1 chr7 87168748 87168749 C, T ABCB1 chr7 87179142 87179143 A, G ABCB1 chr7 87179442 87179443 A, G ABCB1 chr7 87193596 87193597 A, G ABCB1 chr7 87193601 87193602 A, G ABCB1 chr7 87199563 87199564 A, C ABCB1 chr7 87229439 87229440 C, T ABCB1 chr7 87229500 87229501 C, T ABCB1 chr7 90894384 90894385 A, G FZD1 chr7 90895943 90895944 C, T FZD1 chr7 92355032 92355033 A, T CDK6 chr7 93055752 93055753 A, G CALCR chr7 93067398 93067399 G, T CALCR chr7 93070810 93070811 C, T CALCR chr7 93070949 93070950 C, T CALCR chr7 93072952 93072953 C, T CALCR chr7 93097973 93097974 A, G CALCR chr7 93101649 93101650 A, G CALCR chr7 93116298 93116299 A, G CALCR chr7 93125109 93125110 C, T CALCR chr7 99358614 99358615 A, G CYP3A4 chr7 99365942 99365943 A, C CYP3A4 chr7 99367866 99367867 C, G CYP3A4 chr7 100401097 100401098 A, C EPHB4 chr7 100403142 100403143 A, G EPHB4 chr7 100410596 100410597 A, G EPHB4 chr7 100410655 100410656 C, T EPHB4 chr7 100410656 100410657 A, G EPHB4 chr7 100411277 100411278 C, T EPHB4 chr7 100411286 100411287 A, G EPHB4 chr7 100411371 100411372 C, T EPHB4 chr7 100411687 100411688 C, T EPHB4 chr7 100414786 100414787 C, T EPHB4 chr7 100416138 100416139 C, T EPHB4 chr7 100416249 100416250 A, G EPHB4 chr7 100417363 100417364 A, G EPHB4 chr7 100420154 100420155 A, G EPHB4 chr7 100420211 100420212 C, T EPHB4 chr7 100771716 100771717 A, G SERPINE1 chr7 100775204 100775205 C, G SERPINE1 chr7 100775297 100775298 C, T SERPINE1 chr7 100780384 100780385 C, T SERPINE1 chr7 100781407 100781408 C, T SERPINE1 chr7 100781412 100781413 C, T SERPINE1 chr7 100781444 100781445 G, T SERPINE1 chr7 100781467 100781468 A, C SERPINE1 chr7 100781474 100781475 A, C SERPINE1 chr7 105891671 105891672 A, C NAMPT chr7 105903903 105903904 C, T NAMPT chr7 106508977 106508978 A, G PIK3CG chr7 106508986 106508987 C, T PIK3CG chr7 106509330 106509331 A, C PIK3CG chr7 106509932 106509933 A, G PIK3CG chr7 106513010 106513011 C, T PIK3CG chr7 106519942 106519943 C, T PIK3CG chr7 106524688 106524689 C, T PIK3CG chr7 116339281 116339282 A, G MET chr7 116339671 116339672 C, T MET chr7 116340261 116340262 A, G MET chr7 116340268 116340269 C, T MET chr7 116381103 116381104 A, G MET chr7 116397571 116397572 A, G MET chr7 116411866 116411867 A, G MET chr7 116422213 116422214 C, T MET chr7 116435767 116435768 C, T MET chr7 116436021 116436022 A, G MET chr7 116436096 116436097 A, G MET chr7 128828957 128828958 G, T SMO chr7 128843395 128843396 A, G SMO chr7 128845087 128845088 A, G SMO chr7 128846222 128846223 A, G SMO chr7 128851794 128851795 A, C SMO chr7 128851805 128851806 C, G SMO chr7 128851979 128851980 A, G SMO chr7 140426256 140426257 A, G BRAF chr7 140447158 140447159 G, T BRAF chr7 140476935 140476936 A, G BRAF chr7 140477726 140477727 C, T BRAF chr7 140481510 140481511 A, C BRAF chr7 140500334 140500335 C, T BRAF chr7 140624425 140624426 A, C BRAF chr7 142457429 142457430 A, C PRSS1 chr7 142459702 142459703 C PRSS1 chr7 142460393 142460394 T PRSS1 chr7 142460864 142460865 C, T PRSS1 chr7 142561535 142561536 C, T EPHB6 chr7 142562010 142562011 C, T EPHB6 chr7 142562079 142562080 C, T EPHB6 chr7 142562403 142562404 C, T EPHB6 chr7 142563252 142563253 G, T EPHB6 chr7 142563299 142563300 C, T EPHB6 chr7 142564109 142564110 C, T EPHB6 chr7 142565384 142565385 A, G EPHB6 chr7 142565775 142565776 A, G EPHB6 chr7 142566162 142566163 C, G EPHB6 chr7 142566370 142566371 C, T EPHB6 chr7 142567941 142567942 A, G EPHB6 chr7 142568517 142568518 A, G EPHB6 chr7 148504817 148504818 A, G EZH2 chr7 148506362 148506363 G, T EZH2 chr7 148506395 148506396 A, C EZH2 chr7 148508832 148508833 A, G EZH2 chr7 148511170 148511171 C, T EZH2 chr7 148513755 148513756 C, G EZH2 chr7 148514920 148514921 C, T EZH2 chr7 148514933 148514934 A, G EZH2 chr7 148524236 148524237 C, G EZH2 chr7 148525903 148525904 C, G EZH2 chr7 148543524 148543525 A, G EZH2 chr7 151164347 151164348 A, G RHEB chr7 151167603 151167604 A, T RHEB chr7 151168533 151168534 A, G RHEB chr7 151174537 151174538 C, T RHEB chr7 151195312 151195313 A, G RHEB chr7 151195327 151195328 C, G RHEB chr7 152346006 152346007 C, T XRCC2 chr7 152357876 152357877 A, G XRCC2 chr7 152373232 152373233 A, C XRCC2 chr7 152373251 152373252 C, G XRCC2 chr7 155596352 155596353 A, G SHH chr7 155596412 155596413 C, T SHH chr7 155599381 155599382 A, G SHH chr7 155599413 155599414 G SHH chr8 6366573 6366574 A, G ANGPT2 chr8 6371290 6371291 A, G ANGPT2 chr8 6371302 6371303 A, G ANGPT2 chr8 6377432 6377433 C, T ANGPT2 chr8 6378690 6378691 A, G ANGPT2 chr8 6378783 6378784 A, C ANGPT2 chr8 6385066 6385067 G, T ANGPT2 chr8 6385179 6385180 C, T ANGPT2 chr8 6389888 6389889 A, C, G ANGPT2 chr8 6420359 6420360 C, T ANGPT2 chr8 9413874 9413875 C, T TNKS chr8 9413892 9413893 A, G TNKS chr8 9414048 9414049 A, G TNKS chr8 9414158 9414159 C, G TNKS chr8 9537426 9537427 A, G TNKS chr8 9538249 9538250 A, G TNKS chr8 9564309 9564310 C, T TNKS chr8 9564418 9564419 C, T TNKS chr8 9564436 9564437 A, G TNKS chr8 9564484 9564485 A, G TNKS chr8 9564510 9564511 C, T TNKS chr8 9567699 9567700 A, C TNKS chr8 9577939 9577940 C, T TNKS chr8 9627602 9627603 C, T TNKS chr8 9627790 9627791 A, G TNKS chr8 9629780 9629781 A, G TNKS chr8 9629809 9629810 A, G TNKS chr8 9629844 9629845 A, G TNKS chr8 9634151 9634152 C, T TNKS chr8 11612664 11612665 A, T GATA4 chr8 11612697 11612698 A, C GATA4 chr8 11614501 11614502 C, T GATA4 chr8 11614558 11614559 A, G GATA4 chr8 11615927 11615928 A, G GATA4 chr8 18257703 18257704 A, G NAT2 chr8 18257794 18257795 C, T NAT2 chr8 18257853 18257854 C, T NAT2 chr8 18257993 18257994 C, T NAT2 chr8 18258102 18258103 A, G NAT2 chr8 18258315 18258316 A, G NAT2 chr8 18258350 18258351 A, G NAT2 chr8 18258369 18258370 A, G NAT2 chr8 22020258 22020259 A, G SFTPC chr8 22020974 22020975 G, T SFTPC chr8 22021036 22021037 A, C SFTPC chr8 22021795 22021796 A, G SFTPC chr8 22880161 22880162 C, G TNFRSF10B chr8 22880172 22880173 A, G TNFRSF10B chr8 22881851 22881852 C, T TNFRSF10B chr8 22886001 22886002 A, G TNFRSF10B chr8 22886019 22886020 A, G TNFRSF10B chr8 22900700 22900701 A, G TNFRSF10B chr8 22926312 22926313 A, G TNFRSF10B chr8 23049291 23049292 C, T TNFRSF10A chr8 23054634 23054635 A, C TNFRSF10A chr8 23054778 23054779 C, T TNFRSF10A chr8 23054791 23054792 C, T TNFRSF10A chr8 23056903 23056904 G, T TNFRSF10A chr8 23057466 23057467 A, G TNFRSF10A chr8 23058187 23058188 C, T TNFRSF10A chr8 23058219 23058220 G, T TNFRSF10A chr8 23059279 23059280 G, T TNFRSF10A chr8 23059323 23059324 C, G TNFRSF10A chr8 23069573 23069574 C, T TNFRSF10A chr8 23082476 23082477 A, G TNFRSF10A chr8 23155552 23155553 T LOXL2 chr8 23167299 23167300 A, G LOXL2 chr8 23167352 23167353 G, T LOXL2 chr8 23167434 23167435 C, T LOXL2 chr8 23167463 23167464 C, G LOXL2 chr8 23174667 23174668 A, T LOXL2 chr8 23177496 23177497 A, G LOXL2 chr8 23186006 23186007 C, T LOXL2 chr8 23190925 23190926 C, T LOXL2 chr8 23190940 23190941 C, T LOXL2 chr8 23190994 23190995 C, T LOXL2 chr8 23225558 23225559 A, G LOXL2 chr8 23225744 23225745 C, T LOXL2 chr8 23282503 23282504 C LOXL2 chr8 23282556 23282557 C, T LOXL2 chr8 23282560 23282561 C, T LOXL2 chr8 27255262 27255263 A, G PTK2B chr8 27277536 27277537 A, G PTK2B chr8 27277627 27277628 G PTK2B chr8 27279882 27279883 A, G PTK2B chr8 27287996 27287997 A, T PTK2B chr8 27291556 27291557 C, T PTK2B chr8 27293305 27293306 C, T PTK2B chr8 27293334 27293335 G, T PTK2B chr8 27293864 27293865 C, T PTK2B chr8 27294605 27294606 C, G PTK2B chr8 27297744 27297745 A, G PTK2B chr8 27301724 27301725 C, G PTK2B chr8 27308537 27308538 A, G PTK2B chr8 27308584 27308585 A, C PTK2B chr8 27311620 27311621 C, T PTK2B chr8 27311702 27311703 C, T PTK2B chr8 27312134 27312135 A, G PTK2B chr8 27315875 27315876 A, G PTK2B chr8 27315899 27315900 A, G PTK2B chr8 27455840 27455841 A, T CLU chr8 27456129 27456130 A, G CLU chr8 27457478 27457479 C, T CLU chr8 27457506 27457507 C, G CLU chr8 27457511 27457512 G, T CLU chr8 27462480 27462481 A, G CLU chr8 27464080 27464081 C, T CLU chr8 27466577 27466578 G CLU chr8 27467945 27467946 C, T CLU chr8 27467983 27467984 C, T CLU chr8 27468004 27468005 A, G CLU chr8 27469063 27469064 C CLU chr8 27469065 27469066 C, T CLU chr8 27469155 27469156 C, T CLU chr8 27472133 27472134 A, G CLU chr8 27472137 27472138 C, T CLU chr8 27472258 27472259 A, C CLU chr8 37553688 37553689 A, G ZNF703 chr8 37654906 37654907 A, G GPR124 chr8 37655043 37655044 C, G GPR124 chr8 37690614 37690615 A, G GPR124 chr8 37690783 37690784 A, G GPR124 chr8 37692703 37692704 A, G GPR124 chr8 37692730 37692731 C, T GPR124 chr8 37696626 37696627 C, T GPR124 chr8 37697588 37697589 C, G GPR124 chr8 37698901 37698902 C, G GPR124 chr8 37699105 37699106 A, T GPR124 chr8 37699194 37699195 C, G GPR124 chr8 37699393 37699394 C, G GPR124 chr8 37699442 37699443 A, G GPR124 chr8 37699515 37699516 C, T GPR124 chr8 37888089 37888090 C, T EIF4EBP1 chr8 38271300 38271301 A, G FGFR1 chr8 38279247 38279248 A, G FGFR1 chr8 38287237 38287238 A, G FGFR1 chr8 38318714 38318715 A, G FGFR1 chr8 48689365 48689366 C, T PRKDC chr8 48691636 48691637 A, G PRKDC chr8 48694955 48694956 A, G PRKDC chr8 48695174 48695175 C, T PRKDC chr8 48695180 48695181 A, C PRKDC chr8 48697704 48697705 C, T PRKDC chr8 48710879 48710880 C, T PRKDC chr8 48710954 48710955 A, G PRKDC chr8 48715853 48715854 A, G PRKDC chr8 48729958 48729959 C, T PRKDC chr8 48729959 48729960 C, T PRKDC chr8 48739304 48739305 A, G PRKDC chr8 48739338 48739339 A, G PRKDC chr8 48739439 48739440 A, C PRKDC chr8 48771242 48771243 C, T PRKDC chr8 48792041 48792042 A, T PRKDC chr8 48792198 48792199 A, C PRKDC chr8 48794625 48794626 A, C PRKDC chr8 48805787 48805788 C, T PRKDC chr8 48815185 48815186 C, T PRKDC chr8 48817589 48817590 A, G PRKDC chr8 48824964 48824965 C, G PRKDC chr8 48842424 48842425 C, T PRKDC chr8 48843309 48843310 C, G PRKDC chr8 48845530 48845531 C, T PRKDC chr8 48846518 48846519 C, T PRKDC chr8 48852224 48852225 C, T PRKDC chr8 48870029 48870030 A, T PRKDC chr8 56860112 56860113 C, T LYN chr8 56860128 56860129 A, G LYN chr8 56863150 56863151 A, G LYN chr8 56866451 56866452 A, G LYN chr8 56882381 56882382 G LYN chr8 56910927 56910928 C, T LYN chr8 63938763 63938764 A, G GGH chr8 63939838 63939839 C, T GGH chr8 63942716 63942717 C, T GGH chr8 63942732 63942733 C, T GGH chr8 63948197 63948198 A, C GGH chr8 108306154 108306155 C, G ANGPT1 chr8 108315461 108315462 C, T ANGPT1 chr8 108334923 108334924 A, G ANGPT1 chr8 108335012 108335013 A, T ANGPT1 chr8 108335036 108335037 A, T ANGPT1 chr8 108335041 108335042 C, T ANGPT1 chr8 128750539 128750540 A, G MYC chr8 128750606 128750607 A, G MYC chr8 128751200 128751201 A, G MYC chr8 143955915 143955916 C, G CYP11B1 chr8 143956802 143956803 C, G CYP11B1 chr8 143956807 143956808 A, C CYP11B1 chr8 143956853 143956854 A, G CYP11B1 chr8 143957332 143957333 C, G CYP11B1 chr8 143957737 143957738 C, T CYP11B1 chr8 143957824 143957825 A, G CYP11B1 chr8 143958341 143958342 A, G CYP11B1 chr8 143958426 143958427 C, T CYP11B1 chr8 143959187 143959188 A, G, T CYP11B1 chr8 143959218 143959219 A, G CYP11B1 chr8 143959249 143959250 C, T CYP11B1 chr8 143959271 143959272 C, T CYP11B1 chr8 143959288 143959289 C, T CYP11B1 chr8 143959310 143959311 A, G CYP11B1 chr8 143960596 143960597 A, G CYP11B1 chr8 143960625 143960626 A, G CYP11B1 chr8 143961004 143961005 C, T CYP11B1 chr8 143961101 143961102 C, T CYP11B1 chr8 143994040 143994041 C, T CYP11B2 chr8 143994265 143994266 A, G CYP11B2 chr8 143994341 143994342 C, T CYP11B2 chr8 143994805 143994806 A, G, T CYP11B2 chr8 143995742 143995743 C, T CYP11B2 chr8 143995760 143995761 C, T CYP11B2 chr8 143995791 143995792 T CYP11B2 chr8 143996362 143996363 A, G CYP11B2 chr8 143996364 143996365 A, G CYP11B2 chr8 143996538 143996539 C, T CYP11B2 chr8 143996552 143996553 A, G CYP11B2 chr8 143998661 143998662 A, G CYP11B2 chr8 143999145 143999146 C, T CYP11B2 chr8 143999171 143999172 C, T CYP11B2 chr9 5050705 5050706 C, T JAK2 chr9 5066746 5066747 C, T JAK2 chr9 5066785 5066786 C, T JAK2 chr9 5077516 5077517 C, T JAK2 chr9 5081779 5081780 A, G JAK2 chr9 5089687 5089688 C, T JAK2 chr9 5126442 5126443 A, T JAK2 chr9 5457295 5457296 C, T CD274 chr9 5467800 5467801 C, T CD274 chr9 5467924 5467925 A, G CD274 chr9 5549539 5549540 C, T PDCD1LG2 chr9 5557707 5557708 C, T PDCD1LG2 chr9 5557792 5557793 A, T PDCD1LG2 chr9 5563114 5563115 A, T PDCD1LG2 chr9 8319805 8319806 C, T PTPRD chr9 8338877 8338878 A, C PTPRD chr9 8340300 8340301 C, G PTPRD chr9 8340315 8340316 G, T PTPRD chr9 8341184 8341185 A, G PTPRD chr9 8389342 8389343 A, G PTPRD chr9 8389363 8389364 C, G PTPRD chr9 8436702 8436703 C, G PTPRD chr9 8437140 8437141 C, G PTPRD chr9 8454494 8454495 A, G PTPRD chr9 8454565 8454566 C, T PTPRD chr9 8460590 8460591 A, G PTPRD chr9 8465579 8465580 G, T PTPRD chr9 8465597 8465598 A, G PTPRD chr9 8484189 8484190 A, G PTPRD chr9 8484239 8484240 G, T PTPRD chr9 8484297 8484298 A, C PTPRD chr9 8485786 8485787 C, G PTPRD chr9 8485833 8485834 A, G PTPRD chr9 8485927 8485928 A, G PTPRD chr9 8518051 8518052 C, G PTPRD chr9 8518142 8518143 C, T PTPRD chr9 8518394 8518395 A, G PTPRD chr9 8518437 8518438 C, G PTPRD chr9 8518469 8518470 C, G PTPRD chr9 8524853 8524854 C, T PTPRD chr9 21077370 21077371 C, T IFNB1 chr9 21077640 21077641 A, G IFNB1 chr9 21077688 21077689 G, T IFNB1 chr9 21384791 21384792 A, G IFNA2 chr9 21385311 21385312 G, T IFNA2 chr9 21968158 21968159 A, G CDKN2A chr9 21968198 21968199 C, G CDKN2A chr9 21968711 21968712 A, C CDKN2A chr9 21970978 21970979 A, C CDKN2A chr9 21971183 21971184 T CDKN2A chr9 21974437 21974438 C CDKN2A chr9 22006272 22006273 G, T CDKN2B chr9 27157913 27157914 C, T TEK chr9 27158009 27158010 A, G TEK chr9 27168432 27168433 A, G TEK chr9 27168467 27168468 A, G TEK chr9 27168570 27168571 C, T TEK chr9 27173179 27173180 C, T TEK chr9 27183462 27183463 A, C TEK chr9 27183597 27183598 C, T TEK chr9 27190491 27190492 C, T TEK chr9 27190654 27190655 A, G TEK chr9 27197367 27197368 C, T TEK chr9 27203077 27203078 A, G TEK chr9 27203143 27203144 C, T TEK chr9 27205020 27205021 A, G TEK chr9 27213579 27213580 C, T TEK chr9 27213611 27213612 C, G TEK chr9 27218725 27218726 C, T TEK chr9 27220065 27220066 A, G TEK chr9 27220093 27220094 C, T TEK chr9 27220181 27220182 A, T TEK chr9 27228199 27228200 A, G TEK chr9 27229098 27229099 A, G TEK chr9 27229140 27229141 C, T TEK chr9 34655285 34655286 C, T IL11RA chr9 34656727 34656728 A, C IL11RA chr9 34657389 34657390 A, G IL11RA chr9 34657394 34657395 A, G IL11RA chr9 34658477 34658478 C, T IL11RA chr9 34658561 34658562 G IL11RA chr9 34658651 34658652 A, G IL11RA chr9 34661552 34661553 A, G IL11RA chr9 35074916 35074917 C, T FANCG chr9 35075968 35075969 A, G FANCG chr9 35076516 35076517 G FANCG chr9 35076623 35076624 C, T FANCG chr9 35076754 35076755 A, G FANCG chr9 35076905 35076906 C, G FANCG chr9 35076922 35076923 C, T FANCG chr9 35077440 35077441 C, T FANCG chr9 35079360 35079361 G, T FANCG chr9 35079444 35079445 C, T FANCG chr9 35674052 35674053 A, G CA9 chr9 35674100 35674101 C, T CA9 chr9 35674346 35674347 A, T CA9 chr9 35675851 35675852 C, G CA9 chr9 35675960 35675961 A, G CA9 chr9 35676287 35676288 C, T CA9 chr9 35679142 35679143 A, G CA9 chr9 35679250 35679251 A, G CA9 chr9 35680932 35680933 A, G CA9 chr9 36840622 36840623 A, G PAX5 chr9 36840684 36840685 C, T PAX5 chr9 37002805 37002806 A, G PAX5 chr9 37006493 37006494 C, T PAX5 chr9 37015233 37015234 A, G PAX5 chr9 37020621 37020622 A, C PAX5 chr9 80412602 80412603 C, T GNAQ chr9 87338455 87338456 A, G NTRK2 chr9 87339314 87339315 C, T NTRK2 chr9 87342647 87342648 A, C NTRK2 chr9 87356743 87356744 A, G NTRK2 chr9 87356780 87356781 A, C NTRK2 chr9 87366872 87366873 C, T NTRK2 chr9 87563369 87563370 C, T NTRK2 chr9 87636264 87636265 C, T NTRK2 chr9 93606308 93606309 A, G SYK chr9 93626911 93626912 A, G SYK chr9 93626936 93626937 A, C SYK chr9 93629543 93629544 C, T SYK chr9 93636430 93636431 A, G SYK chr9 93637014 93637015 C, T SYK chr9 93639845 93639846 A, C, G SYK chr9 93639848 93639849 A, G SYK chr9 93639972 93639973 C, G SYK chr9 93640008 93640009 A, G SYK chr9 93641150 93641151 C, T SYK chr9 93641174 93641175 C, T SYK chr9 93641198 93641199 C, T SYK chr9 93650014 93650015 A, T SYK chr9 93657760 93657761 A, T SYK chr9 97869395 97869396 C FANCC chr9 97897654 97897655 A, G FANCC chr9 97934358 97934359 C, T FANCC chr9 97934366 97934367 C, T FANCC chr9 98011601 98011602 G, T FANCC chr9 98209593 98209594 A, G PTCH1 chr9 98209692 98209693 A, G PTCH1 chr9 98209741 98209742 A, G PTCH1 chr9 98211548 98211549 A, G PTCH1 chr9 98211571 98211572 A, T PTCH1 chr9 98211587 98211588 G PTCH1 chr9 98215821 98215822 A, G PTCH1 chr9 98215967 98215968 C, G PTCH1 chr9 98220321 98220322 A, C PTCH1 chr9 98229388 98229389 C, G PTCH1 chr9 98231099 98231100 A, G PTCH1 chr9 98231345 98231346 C, G PTCH1 chr9 98236303 98236304 C, T PTCH1 chr9 98236308 98236309 C, T PTCH1 chr9 98236396 98236397 A, G PTCH1 chr9 98238357 98238358 A, G PTCH1 chr9 98239146 98239147 A, G PTCH1 chr9 98239189 98239190 C, G PTCH1 chr9 98241377 98241378 A, G PTCH1 chr9 98278939 98278940 C, G PTCH1 chr9 101890979 101890980 A, G TGFBR1 chr9 101908914 101908915 A, G TGFBR1 chr9 110249504 110249505 C, T KLF4 chr9 110250170 110250171 A, G KLF4 chr9 117782890 117782891 C, T TNC chr9 117791616 117791617 C, T TNC chr9 117791663 117791664 C, T TNC chr9 117791708 117791709 A, G TNC chr9 117792598 117792599 C, T TNC chr9 117797524 117797525 G, T TNC chr9 117797596 117797597 C, T TNC chr9 117803270 117803271 C, T TNC chr9 117803379 117803380 C, G TNC chr9 117804543 117804544 C, T TNC chr9 117804552 117804553 C, T TNC chr9 117804666 117804667 C, T TNC chr9 117808784 117808785 A, T TNC chr9 117815010 117815011 C, T TNC chr9 117815035 117815036 A, G TNC chr9 117827037 117827038 G, T TNC chr9 117827059 117827060 C, T TNC chr9 117835930 117835931 A, G TNC chr9 117840275 117840276 C, T TNC chr9 117840333 117840334 A, G TNC chr9 117844019 117844020 C, T TNC chr9 117844065 117844066 G, T TNC chr9 117845010 117845011 C, T TNC chr9 117846569 117846570 C, T TNC chr9 117846579 117846580 C, T TNC chr9 117848196 117848197 C, T TNC chr9 117848393 117848394 C, T TNC chr9 117849228 117849229 C, T TNC chr9 117849313 117849314 C, T TNC chr9 117849372 117849373 C, T TNC chr9 117853021 117853022 C, T TNC chr9 117853222 117853223 C, G TNC chr9 120474720 120474721 C, T TLR4 chr9 120475301 120475302 A, G TLR4 chr9 120475601 120475602 C, T TLR4 chr9 120475825 120475826 A, G TLR4 chr9 120475935 120475936 G, T TLR4 chr9 128000647 128000648 A, C HSPA5 chr9 128001118 128001119 C, T HSPA5 chr9 130549076 130549077 A, G CDK9 chr9 130549789 130549790 C, T CDK9 chr9 130550197 130550198 C, G CDK9 chr9 130550486 130550487 C, T CDK9 chr9 130551710 130551711 C, T CDK9 chr9 130578005 130578006 A, G ENG chr9 130578279 130578280 A, G ENG chr9 130580938 130580939 C, T ENG chr9 130586620 130586621 C, G ENG chr9 130586656 130586657 A, G ENG chr9 130586687 130586688 A, G ENG chr9 130588153 130588154 A, G ENG chr9 130588168 130588169 C, T ENG chr9 130616620 130616621 A, G ENG chr9 132580900 132580901 C, G TOR1A chr9 132586415 132586416 A, C TOR1A chr9 133710245 133710246 A, T ABL1 chr9 133730137 133730138 A, G ABL1 chr9 133738319 133738320 A, G ABL1 chr9 133747456 133747457 C, T ABL1 chr9 133748201 133748202 C, T ABL1 chr9 133755527 133755528 A, G ABL1 chr9 133759545 133759546 A, G ABL1 chr9 133760028 133760029 C, G ABL1 chr9 133760591 133760592 C, T ABL1 chr9 133760616 133760617 C, T ABL1 chr9 133760676 133760677 C, T ABL1 chr9 133761000 133761001 A, G ABL1 chr9 135771729 135771730 A, G TSC1 chr9 135771792 135771793 A, G TSC1 chr9 135776924 135776925 C, T TSC1 chr9 135781204 135781205 C, T TSC1 chr9 135781238 135781239 A, G TSC1 chr9 135782220 135782221 C, T TSC1 chr9 135786903 135786904 A, G TSC1 chr9 135804138 135804139 C, T TSC1 chr9 139390675 139390676 A, C NOTCH1 chr9 139390957 139390958 C, T NOTCH1 chr9 139391199 139391200 C, T NOTCH1 chr9 139391337 139391338 C, T NOTCH1 chr9 139391413 139391414 A, G NOTCH1 chr9 139391635 139391636 A, G NOTCH1 chr9 139391736 139391737 C, G NOTCH1 chr9 139393306 139393307 A, G NOTCH1 chr9 139396407 139396408 A, G NOTCH1 chr9 139397706 139397707 A, G NOTCH1 chr9 139399131 139399132 C, T NOTCH1 chr9 139399319 139399320 C, T NOTCH1 chr9 139401288 139401289 C, G NOTCH1 chr9 139401301 139401302 A, G NOTCH1 chr9 139402379 139402380 A, C NOTCH1 chr9 139402657 139402658 C, T NOTCH1 chr9 139402662 139402663 C, T NOTCH1 chr9 139402693 139402694 A, C NOTCH1 chr9 139404171 139404172 A, G NOTCH1 chr9 139405092 139405093 A, G NOTCH1 chr9 139405741 139405742 C, T NOTCH1 chr9 139407931 139407932 A, G NOTCH1 chr9 139408963 139408964 A, G NOTCH1 chr9 139410588 139410589 A, G NOTCH1 chr9 139411872 139411873 A, G NOTCH1 chr9 139411879 139411880 A, G NOTCH1 chr9 139413268 139413269 A, G NOTCH1 chr9 139413907 139413908 C, T NOTCH1 chr9 139417332 139417333 A, G NOTCH1 chr9 139417380 139417381 A, G NOTCH1 chr9 139418259 139418260 A, G NOTCH1 chr9 139438410 139438411 C, G NOTCH1 chr9 139562992 139562993 C, T EGFL7 chr9 139564105 139564106 C, G EGFL7 chr9 139564473 139564474 C, G EGFL7 chr9 139564667 139564668 A, G EGFL7 chr9 139566777 139566778 C, T EGFL7 chr10 6060056 6060057 A, G IL2RA chr10 6061406 6061407 C, T IL2RA chr10 6061478 6061479 A, C IL2RA chr10 6061498 6061499 C, T IL2RA chr10 6061780 6061781 C, T IL2RA chr10 6063507 6063508 A, G IL2RA chr10 6063566 6063567 C, T IL2RA chr10 6063673 6063674 C, T IL2RA chr10 8100631 8100632 C, T GATA3 chr10 8100646 8100647 C, T GATA3 chr10 8106134 8106135 A, G GATA3 chr10 8111408 8111409 C, T GATA3 chr10 8115907 8115908 A, G GATA3 chr10 22615321 22615322 A, G BMI1 chr10 22617644 22617645 C, T BMI1 chr10 33190566 33190567 A, C ITGB1 chr10 33200497 33200498 A, G ITGB1 chr10 33200557 33200558 A, G ITGB1 chr10 33200781 33200782 C, T ITGB1 chr10 33208943 33208944 C, T ITGB1 chr10 33209265 33209266 G, T ITGB1 chr10 33211226 33211227 G, T ITGB1 chr10 33214801 33214802 A, G ITGB1 chr10 33215060 33215061 A, T ITGB1 chr10 33217109 33217110 A, G ITGB1 chr10 35929130 35929131 A, G FZD8 chr10 35929139 35929140 A, G FZD8 chr10 35929349 35929350 C, T FZD8 chr10 43595967 43595968 A, G RET chr10 43596032 43596033 A, G RET chr10 43600606 43600607 A, C RET chr10 43600688 43600689 A, G RET chr10 43606649 43606650 C, T RET chr10 43606686 43606687 A, G RET chr10 43606855 43606856 A, G RET chr10 43608432 43608433 C RET chr10 43610118 43610119 A, G RET chr10 43613842 43613843 G, T RET chr10 43615093 43615094 C, T RET chr10 43615632 43615633 C, G RET chr10 43620366 43620367 A, G RET chr10 43622216 43622217 C, T RET chr10 44793298 44793299 C, T CXCL12 chr10 44793354 44793355 A, G CXCL12 chr10 44868855 44868856 A, C CXCL12 chr10 44868863 44868864 C, T CXCL12 chr10 44871547 44871548 A, G CXCL12 chr10 44873212 44873213 G, T CXCL12 chr10 48414515 48414516 A, T GDF2 chr10 48416337 48416338 A, G GDF2 chr10 54074756 54074757 A, G DKK1 chr10 54076270 54076271 A, G DKK1 chr10 54076310 54076311 C, T DKK1 chr10 62551888 62551889 A, G CDK1 chr10 70332579 70332580 A, G TET1 chr10 70332671 70332672 A, T TET1 chr10 70332861 70332862 C, T TET1 chr10 70333397 70333398 A, G TET1 chr10 70333554 70333555 C, T TET1 chr10 70404980 70404981 A, G TET1 chr10 70405236 70405237 A, G TET1 chr10 70405438 70405439 G, T TET1 chr10 70405538 70405539 A, G TET1 chr10 70405854 70405855 A, G TET1 chr10 70405900 70405901 C, T TET1 chr10 70406746 70406747 A, G TET1 chr10 70411535 70411536 A, G TET1 chr10 70432643 70432644 C, T TET1 chr10 70451546 70451547 A, G TET1 chr10 74714293 74714294 A, G PLA2G12B chr10 75671397 75671398 A, C PLAU chr10 75671404 75671405 A, G PLAU chr10 75671570 75671571 C, T PLAU chr10 75671702 75671703 A, G PLAU chr10 75671874 75671875 A, G PLAU chr10 75673100 75673101 C, T PLAU chr10 75673730 75673731 C, T PLAU chr10 75673747 75673748 A, C PLAU chr10 89653685 89653686 A, G PTEN chr10 90749255 90749256 A, G FAS chr10 90750599 90750600 A, G FAS chr10 90762800 90762801 A, G FAS chr10 90762857 90762858 C, T FAS chr10 90762895 90762896 A, G FAS chr10 90767481 90767482 A, G FAS chr10 90771828 90771829 C, T FAS chr10 90773198 90773199 A, G FAS chr10 94353277 94353278 G, T KIF11 chr10 94366834 94366835 G, T KIF11 chr10 94366897 94366898 A, G KIF11 chr10 94392325 94392326 A, C KIF11 chr10 94393482 94393483 A, G KIF11 chr10 94397294 94397295 A, T KIF11 chr10 94409748 94409749 C, T KIF11 chr10 94413507 94413508 C, G KIF11 chr10 96534767 96534768 A, G CYP2C19 chr10 96540409 96540410 A, G CYP2C19 chr10 96541615 96541616 A, G CYP2C19 chr10 96602621 96602622 C, T CYP2C19 chr10 96602622 96602623 A, G CYP2C19 chr10 96609774 96609775 A, C CYP2C19 chr10 96701600 96701601 C, G CYP2C9 chr10 96702046 96702047 C, T CYP2C9 chr10 96702065 96702066 A, G CYP2C9 chr10 96708973 96708974 A, G CYP2C9 chr10 96740907 96740908 C, T CYP2C9 chr10 96740980 96740981 C, T CYP2C9 chr10 96741164 96741165 C, T CYP2C9 chr10 96748736 96748737 A, T CYP2C9 chr10 96798714 96798715 A, G CYP2C8 chr10 96798748 96798749 C, T CYP2C8 chr10 96802736 96802737 A, G CYP2C8 chr10 96818118 96818119 C, G CYP2C8 chr10 96827117 96827118 A, G CYP2C8 chr10 96827149 96827150 C, T CYP2C8 chr10 96827177 96827178 C, T CYP2C8 chr10 96827484 96827485 A, G CYP2C8 chr10 101542577 101542578 C, T ABCC2 chr10 101544446 101544447 T ABCC2 chr10 101560168 101560169 A, G ABCC2 chr10 101563784 101563785 C, T ABCC2 chr10 101563814 101563815 A, G ABCC2 chr10 101567785 101567786 A, T ABCC2 chr10 101569996 101569997 C, T ABCC2 chr10 101571441 101571442 G, T ABCC2 chr10 101577034 101577035 A, T ABCC2 chr10 101590618 101590619 C, T ABCC2 chr10 101591417 101591418 A, G ABCC2 chr10 101595974 101595975 G, T ABCC2 chr10 101595995 101595996 A, T ABCC2 chr10 101603521 101603522 C, T ABCC2 chr10 101603630 101603631 A ABCC2 chr10 101604106 101604107 C, T ABCC2 chr10 101605454 101605455 C, T ABCC2 chr10 101605502 101605503 C, T ABCC2 chr10 101606860 101606861 G, T ABCC2 chr10 101610454 101610455 A, G ABCC2 chr10 101610532 101610533 C, T ABCC2 chr10 101611293 101611294 A, G ABCC2 chr10 104264106 104264107 C, T SUFU chr10 104353324 104353325 C, G SUFU chr10 104386933 104386934 C, T SUFU chr10 104591392 104591393 G, T CYP17A1 chr10 104596923 104596924 A, C CYP17A1 chr10 104596980 104596981 A, G CYP17A1 chr10 106014724 106014725 A, G GSTO1 chr10 106019568 106019569 G, T GSTO1 chr10 106022788 106022789 A, C GSTO1 chr10 106025989 106025990 G, T GSTO1 chr10 106027058 106027059 A, G GSTO1 chr10 106034614 106034615 G, T GSTO2 chr10 106035131 106035132 A, G GSTO2 chr10 106035132 106035133 A, C GSTO2 chr10 106039089 106039090 A, C GSTO2 chr10 106039184 106039185 A, G GSTO2 chr10 106045777 106045778 C, T GSTO2 chr10 106058939 106058940 C, T GSTO2 chr10 115451780 115451781 C, T CASP7 chr10 115480756 115480757 C, T CASP7 chr10 115480935 115480936 A, G CASP7 chr10 115481470 115481471 C, T CASP7 chr10 115489151 115489152 C, G CASP7 chr10 115489166 115489167 A, G CASP7 chr10 123239111 123239112 A, G FGFR2 chr10 123243196 123243197 A, G FGFR2 chr10 123247549 123247550 A, G FGFR2 chr10 123277600 123277601 A, G FGFR2 chr10 123298157 123298158 C, T FGFR2 chr10 123310870 123310871 A, G FGFR2 chr10 123324176 123324177 C, T FGFR2 chr10 123325157 123325158 A, G FGFR2 chr10 123353212 123353213 A, C FGFR2 chr10 131265544 131265545 C, T MGMT chr10 131265641 131265642 C, T MGMT chr10 131265664 131265665 G, T MGMT chr10 131506310 131506311 A, G MGMT chr10 131565169 131565170 A, G MGMT chr11 534196 534197 C, T HRAS chr11 534241 534242 A, G HRAS chr11 838012 838013 C, T CD151 chr11 838109 838110 C, T CD151 chr11 2185555 2185556 A, G TH chr11 2186423 2186424 A, G TH chr11 2186517 2186518 C, T TH chr11 2187721 2187722 A, C TH chr11 2187854 2187855 C, G TH chr11 2188237 2188238 C, T TH chr11 2188788 2188789 A, T TH chr11 2189184 2189185 A, G TH chr11 2189903 2189904 A, G TH chr11 2190924 2190925 C, T TH chr11 2190950 2190951 C, T TH chr11 2190981 2190982 A, G TH chr11 2191005 2191006 C, T TH chr11 5247790 5247791 C, G HBB chr11 13514023 13514024 C, T PTH chr11 13514052 13514053 G, T PTH chr11 13514256 13514257 C, T PTH chr11 13514262 13514263 C, T PTH chr11 13514307 13514308 A, C PTH chr11 14991538 14991539 C, T CALCA chr11 22646570 22646571 C, T FANCF chr11 22646732 22646733 A, C FANCF chr11 22647260 22647261 A, G FANCF chr11 32410773 32410774 A, G WT1 chr11 32421532 32421533 C, T WT1 chr11 32421653 32421654 C, T WT1 chr11 32449623 32449624 A, C WT1 chr11 32449660 32449661 A, G WT1 chr11 32452031 32452032 C, G WT1 chr11 32456297 32456298 A, G WT1 chr11 32456561 32456562 A, G WT1 chr11 32456693 32456694 A, C WT1 chr11 35160838 35160839 A, G CD44 chr11 35198107 35198108 A, G CD44 chr11 35201809 35201810 C, T CD44 chr11 35201841 35201842 C, T CD44 chr11 35201957 35201958 A, G CD44 chr11 35201960 35201961 T CD44 chr11 35222680 35222681 C, T CD44 chr11 35222758 35222759 A, G CD44 chr11 35223302 35223303 A, G CD44 chr11 35226154 35226155 A, G CD44 chr11 35229672 35229673 C, T CD44 chr11 35231626 35231627 C, T CD44 chr11 35236385 35236386 C, T CD44 chr11 35250714 35250715 C, T CD44 chr11 46740870 46740871 A, G F2 chr11 46740906 46740907 C, G F2 chr11 46742248 46742249 C, T F2 chr11 46744924 46744925 C, G F2 chr11 46744988 46744989 C, T F2 chr11 46745002 46745003 C, T F2 chr11 46749647 46749648 A, G F2 chr11 46760755 46760756 A, G F2 chr11 49168415 49168416 A, G FOLH1 chr11 49176056 49176057 C, T FOLH1 chr11 49176057 49176058 A, G FOLH1 chr11 49194889 49194890 A, T FOLH1 chr11 49194893 49194894 A, G FOLH1 chr11 49196489 49196490 C, T FOLH1 chr11 49197415 49197416 A, G FOLH1 chr11 49207314 49207315 A, G FOLH1 chr11 49208177 49208178 A, T FOLH1 chr11 49214393 49214394 A, G FOLH1 chr11 49221884 49221885 A, T FOLH1 chr11 49227619 49227620 A, G FOLH1 chr11 49228386 49228387 C, T FOLH1 chr11 60229969 60229970 A, G MS4A1 chr11 60230530 60230531 C, T MS4A1 chr11 64003433 64003434 A, G VEGFB chr11 64003671 64003672 C, T VEGFB chr11 64004642 64004643 C, G VEGFB chr11 64004648 64004649 G, T VEGFB chr11 64004691 64004692 C, T VEGFB chr11 64004730 64004731 A, G VEGFB chr11 64004923 64004924 G VEGFB chr11 64004934 64004935 A, G VEGFB chr11 64037678 64037679 A, G BAD chr11 64039174 64039175 A, G BAD chr11 64051852 64051853 A, G BAD chr11 64572017 64572018 C, T MEN1 chr11 64572556 64572557 A, G MEN1 chr11 64572601 64572602 A, G MEN1 chr11 64577146 64577147 A, G MEN1 chr11 66082181 66082182 A, T CD248 chr11 66082212 66082213 A, G CD248 chr11 66082427 66082428 G, T CD248 chr11 66083128 66083129 C, T CD248 chr11 66083157 66083158 A, G CD248 chr11 66083268 66083269 A, G CD248 chr11 66083361 66083362 A, G CD248 chr11 66083781 66083782 A, G CD248 chr11 66084155 66084156 C, T CD248 chr11 66084243 66084244 A, G CD248 chr11 66084330 66084331 A, G CD248 chr11 67351296 67351297 A, G GSTP1 chr11 67351584 67351585 C, G GSTP1 chr11 67351673 67351674 A, G GSTP1 chr11 67352160 67352161 C, T GSTP1 chr11 67352255 67352256 A, C GSTP1 chr11 67352688 67352689 A, G GSTP1 chr11 67353578 67353579 C, T GSTP1 chr11 67353841 67353842 A, G GSTP1 chr11 67353843 67353844 C, T GSTP1 chr11 67353969 67353970 C, T GSTP1 chr11 69458904 69458905 A, G CCND1 chr11 69462855 69462856 C, T CCND1 chr11 69462909 69462910 A, G CCND1 chr11 69465859 69465860 A, G CCND1 chr11 69588728 69588729 A, G FGF4 chr11 69589555 69589556 A, G FGF4 chr11 69625384 69625385 C, T FGF3 chr11 69625472 69625473 A, G FGF3 chr11 69633632 69633633 A, C FGF3 chr11 88911234 88911235 A, G TYR chr11 88911298 88911299 C, T TYR chr11 88911695 88911696 A, C TYR chr11 89017960 89017961 A, G TYR chr11 94153325 94153326 C, T MRE11A chr11 94153399 94153400 A, C MRE11A chr11 94168987 94168988 C, T MRE11A chr11 94200961 94200962 A, G MRE11A chr11 94201044 94201045 A, C MRE11A chr11 94209424 94209425 C, G MRE11A chr11 94209612 94209613 A, G MRE11A chr11 94212047 94212048 C, T MRE11A chr11 94225919 94225920 C, T MRE11A chr11 100909990 100909991 C, T PGR chr11 100921664 100921665 A, C PGR chr11 100922201 100922202 A, G PGR chr11 100933411 100933412 A, C PGR chr11 100962527 100962528 G, T PGR chr11 100998471 100998472 A, C PGR chr11 100998622 100998623 A, G PGR chr11 100998761 100998762 C, G PGR chr11 100998770 100998771 C, G PGR chr11 100999012 100999013 C, T PGR chr11 100999189 100999190 A, G PGR chr11 100999240 100999241 C, T PGR chr11 100999653 100999654 C, T PGR chr11 100999654 100999655 C, T PGR chr11 102195500 102195501 A, G BIRC3 chr11 102196018 102196019 A, G BIRC3 chr11 102196176 102196177 C, T BIRC3 chr11 102199612 102199613 A, T BIRC3 chr11 102201847 102201848 A, G BIRC3 chr11 102207592 102207593 C, T BIRC3 chr11 102248376 102248377 C, T BIRC2 chr11 106810557 106810558 A, G GUCY1A2 chr11 106849396 106849397 C, T GUCY1A2 chr11 106849399 106849400 A, G GUCY1A2 chr11 108106442 108106443 A, T ATM chr11 108114726 108114727 C, G ATM chr11 108114748 108114749 A, G ATM chr11 108114751 108114752 A, T ATM chr11 108114839 108114840 C, T ATM chr11 108119769 108119770 C, G ATM chr11 108121732 108121733 A, G ATM chr11 108122591 108122592 C, G ATM chr11 108127009 108127010 C, T ATM chr11 108129656 108129657 A, G ATM chr11 108129777 108129778 A, C ATM chr11 108138044 108138045 C, T ATM chr11 108139182 108139183 A, G ATM chr11 108143298 108143299 A, G ATM chr11 108143455 108143456 C, G ATM chr11 108150315 108150316 A, G ATM chr11 108159731 108159732 C, T ATM chr11 108163486 108163487 C, T ATM chr11 108175461 108175462 A, G ATM chr11 108186652 108186653 C, T ATM chr11 108192158 108192159 G, T ATM chr11 108198390 108198391 C, T ATM chr11 108204517 108204518 A, C ATM chr11 108225660 108225661 A, G ATM chr11 118343847 118343848 C, T MLL chr11 118348962 118348963 G, T MLL chr11 118361853 118361854 C, T MLL chr11 118367006 118367007 G, T MLL chr11 118373570 118373571 A, T MLL chr11 118374295 118374296 A, G MLL chr11 118374646 118374647 C, T MLL chr11 118375567 118375568 A, T MLL chr11 118375997 118375998 A, G MLL chr11 118376815 118376816 A, G MLL chr11 118377296 118377297 C, T MLL chr11 119145666 119145667 A, G CBL chr11 119148572 119148573 G, T CBL chr11 119155885 119155886 C, T CBL chr11 119156192 119156193 C, T CBL chr11 119170361 119170362 C, T CBL chr11 125495718 125495719 A, G CHEK1 chr11 125495739 125495740 A, G CHEK1 chr11 125495745 125495746 C, G CHEK1 chr11 125497465 125497466 G, T CHEK1 chr11 125507276 125507277 C, T CHEK1 chr11 125523666 125523667 A, G CHEK1 chr12 401879 401880 A, T KDM5A chr12 404857 404858 C, G KDM5A chr12 406291 406292 A, G KDM5A chr12 416292 416293 C, T KDM5A chr12 420069 420070 A, G KDM5A chr12 427574 427575 A, G KDM5A chr12 432758 432759 C, T KDM5A chr12 438071 438072 C, T KDM5A chr12 461373 461374 C, G KDM5A chr12 463247 463248 C, G KDM5A chr12 465614 465615 C KDM5A chr12 498284 498285 C, T KDM5A chr12 4388083 4388084 C, G CCND2 chr12 4479548 4479549 A, G FGF23 chr12 4543360 4543361 A, G FGF6 chr12 4543486 4543487 A, T FGF6 chr12 4553331 4553332 A, G FGF6 chr12 4553382 4553383 A, G FGF6 chr12 4554547 4554548 C, G FGF6 chr12 4554629 4554630 A, G FGF6 chr12 6058402 6058403 A, G VWF chr12 6058912 6058913 A, G VWF chr12 6058919 6058920 A, G VWF chr12 6060959 6060960 A, G VWF chr12 6061068 6061069 G, T VWF chr12 6061558 6061559 C, T VWF chr12 6061674 6061675 A, G VWF chr12 6062776 6062777 A, G VWF chr12 6077215 6077216 A, G VWF chr12 6078407 6078408 C, T VWF chr12 6080931 6080932 A, C VWF chr12 6085444 6085445 A, G VWF chr12 6085446 6085447 A, G VWF chr12 6090999 6091000 A, G VWF chr12 6092441 6092442 A, G VWF chr12 6094289 6094290 A, T VWF chr12 6094783 6094784 C, T VWF chr12 6094844 6094845 A, G VWF chr12 6103071 6103072 C, T VWF chr12 6103280 6103281 A, T VWF chr12 6120957 6120958 A, G VWF chr12 6122751 6122752 A, G VWF chr12 6125819 6125820 A, G VWF chr12 6128169 6128170 C, G VWF chr12 6128279 6128280 C, T VWF chr12 6128442 6128443 C, T VWF chr12 6128445 6128446 C, T VWF chr12 6128788 6128789 C, T VWF chr12 6128891 6128892 C VWF chr12 6131160 6131161 A, G VWF chr12 6131957 6131958 C, T VWF chr12 6131958 6131959 A, G VWF chr12 6132017 6132018 A, G VWF chr12 6132029 6132030 A, G VWF chr12 6132783 6132784 C, T VWF chr12 6132789 6132790 G, T VWF chr12 6134714 6134715 A, G VWF chr12 6138574 6138575 C, T VWF chr12 6138594 6138595 C, T VWF chr12 6143983 6143984 C, T VWF chr12 6145589 6145590 G, T VWF chr12 6145648 6145649 A, T VWF chr12 6153513 6153514 A, G VWF chr12 6153533 6153534 C, T VWF chr12 6153658 6153659 G, T VWF chr12 6155949 6155950 C, T VWF chr12 6166173 6166174 A, G VWF chr12 6167117 6167118 C, T VWF chr12 6167195 6167196 A, G VWF chr12 6172201 6172202 C, T VWF chr12 6172229 6172230 A, G VWF chr12 6173432 6173433 C, T VWF chr12 6173514 6173515 A, G VWF chr12 6174413 6174414 G, T VWF chr12 6174422 6174423 A, T VWF chr12 6180581 6180582 A, T VWF chr12 6181634 6181635 A, G VWF chr12 6182752 6182753 C, T VWF chr12 6182827 6182828 A, T VWF chr12 6204614 6204615 G, T VWF chr12 6219681 6219682 A, G VWF chr12 6219986 6219987 A, C VWF chr12 6232425 6232426 A, G VWF chr12 6883721 6883722 C, T LAG3 chr12 6887019 6887020 C, T LAG3 chr12 6909387 6909388 A, G CD4 chr12 6923461 6923462 C, T CD4 chr12 6924121 6924122 A, G CD4 chr12 6925148 6925149 C, T CD4 chr12 6925293 6925294 C, T CD4 chr12 6925312 6925313 G, T CD4 chr12 6925406 6925407 C, T CD4 chr12 6926362 6926363 C, T CD4 chr12 6927664 6927665 C, T CD4 chr12 6928074 6928075 C, T CD4 chr12 6928485 6928486 C, T CD4 chr12 11992167 11992168 A, G ETV6 chr12 12043862 12043863 C, T ETV6 chr12 12312795 12312796 A, G LRP6 chr12 12317519 12317520 G, T LRP6 chr12 12317520 12317521 C, T LRP6 chr12 12332841 12332842 C, T LRP6 chr12 12334005 12334006 C, G LRP6 chr12 12336965 12336966 A, G LRP6 chr12 12337060 12337061 C, T LRP6 chr12 12397265 12397266 A, T LRP6 chr12 12871098 12871099 G, T CDKN1B chr12 12874141 12874142 C, T CDKN1B chr12 21325759 21325760 C, G SLCO1B1 chr12 21327666 21327667 A, C SLCO1B1 chr12 21329737 21329738 A, G SLCO1B1 chr12 21329760 21329761 A, G SLCO1B1 chr12 21329812 21329813 A, C SLCO1B1 chr12 21329831 21329832 G, T SLCO1B1 chr12 21331548 21331549 C, T SLCO1B1 chr12 21331598 21331599 C, T SLCO1B1 chr12 21331624 21331625 C, T SLCO1B1 chr12 21331859 21331860 A, G SLCO1B1 chr12 21331986 21331987 C, T SLCO1B1 chr12 21349884 21349885 A, G SLCO1B1 chr12 21350033 21350034 A, G SLCO1B1 chr12 21353556 21353557 C, T SLCO1B1 chr12 21353628 21353629 A, G SLCO1B1 chr12 21355488 21355489 C, G SLCO1B1 chr12 21355536 21355537 A, G SLCO1B1 chr12 21358921 21358922 C, T SLCO1B1 chr12 21358932 21358933 C, G SLCO1B1 chr12 21375158 21375159 A, G SLCO1B1 chr12 21377701 21377702 A, G SLCO1B1 chr12 25362853 25362854 C, T KRAS chr12 46125128 46125129 G, T ARID2 chr12 46149586 46149587 A ARID2 chr12 46215162 46215163 A, G ARID2 chr12 46244416 46244417 A, T ARID2 chr12 46244669 46244670 A, G ARID2 chr12 46245076 46245077 A, G ARID2 chr12 46246093 46246094 A, G ARID2 chr12 46246205 46246206 G, T ARID2 chr12 46246397 46246398 A, G ARID2 chr12 46285748 46285749 A, G ARID2 chr12 48238756 48238757 A, G VDR chr12 48249387 48249388 C VDR chr12 48251075 48251076 C, T VDR chr12 48251304 48251305 A, G VDR chr12 48272742 48272743 A, G VDR chr12 48272839 48272840 A, G VDR chr12 48272848 48272849 A, G VDR chr12 48298294 48298295 A, G VDR chr12 49418434 49418435 A, C MLL2 chr12 49422794 49422795 A, G MLL2 chr12 49422825 49422826 A, G MLL2 chr12 49422856 49422857 C, T MLL2 chr12 49424533 49424534 A, G MLL2 chr12 49424615 49424616 A, G MLL2 chr12 49424864 49424865 C, T MLL2 chr12 49425442 49425443 C, G MLL2 chr12 49425977 49425978 C, T MLL2 chr12 49426459 49426460 A, G MLL2 chr12 49426877 49426878 C, T MLL2 chr12 49427918 49427919 C, T MLL2 chr12 49428322 49428323 A, G MLL2 chr12 49431093 49431094 C, T MLL2 chr12 49433355 49433356 A, G MLL2 chr12 49433414 49433415 A, G MLL2 chr12 49434073 49434074 A, C MLL2 chr12 49434364 49434365 A, G MLL2 chr12 49434408 49434409 A, G MLL2 chr12 49434745 49434746 A, G MLL2 chr12 49435813 49435814 C, T MLL2 chr12 49435823 49435824 A, C MLL2 chr12 49436004 49436005 C, T MLL2 chr12 49437398 49437399 G, T MLL2 chr12 49438163 49438164 C, T MLL2 chr12 49438252 49438253 A, G MLL2 chr12 49438346 49438347 C, T MLL2 chr12 49441904 49441905 C, G MLL2 chr12 49444544 49444545 A, G MLL2 chr12 49445027 49445028 A, G MLL2 chr12 49445215 49445216 C, T MLL2 chr12 49445527 49445528 C, G MLL2 chr12 49446039 49446040 C, T MLL2 chr12 49448462 49448463 C, T MLL2 chr12 52306340 52306341 A, G ACVRL1 chr12 52307027 52307028 C, T ACVRL1 chr12 52307144 52307145 C, T ACVRL1 chr12 52308343 52308344 A, G ACVRL1 chr12 52308392 52308393 C ACVRL1 chr12 52309901 52309902 A, G ACVRL1 chr12 52310025 52310026 C, T ACVRL1 chr12 52310035 52310036 C, T ACVRL1 chr12 52312943 52312944 C, T ACVRL1 chr12 52435631 52435632 A, C NR4A1 chr12 52435690 52435691 A, G NR4A1 chr12 52435743 52435744 C, T NR4A1 chr12 52448156 52448157 A, G NR4A1 chr12 52448187 52448188 C, G NR4A1 chr12 52448730 52448731 C, T NR4A1 chr12 52448858 52448859 C, T NR4A1 chr12 52449026 52449027 A, G NR4A1 chr12 52450383 52450384 A, G NR4A1 chr12 52450479 52450480 C, T NR4A1 chr12 52450830 52450831 A, G NR4A1 chr12 52450934 52450935 A, G NR4A1 chr12 52452605 52452606 C, T NR4A1 chr12 52452756 52452757 C, T NR4A1 chr12 54795409 54795410 A, G ITGA5 chr12 54795844 54795845 A, G ITGA5 chr12 54796756 54796757 C, T ITGA5 chr12 54796997 54796998 A, G ITGA5 chr12 54797041 54797042 G ITGA5 chr12 54797570 54797571 C, G ITGA5 chr12 54798008 54798009 A, G ITGA5 chr12 54798010 54798011 C, T ITGA5 chr12 54798011 54798012 A, G ITGA5 chr12 54798047 54798048 A, G ITGA5 chr12 54798692 54798693 A, G ITGA5 chr12 54799681 54799682 C, T ITGA5 chr12 54801524 54801525 A, G ITGA5 chr12 54802029 54802030 G, T ITGA5 chr12 54802579 54802580 A, G ITGA5 chr12 54802637 54802638 A, G ITGA5 chr12 54802669 54802670 C, G ITGA5 chr12 54805752 54805753 G, T ITGA5 chr12 54805764 54805765 C, T ITGA5 chr12 56360875 56360876 A, G CDK2 chr12 56363356 56363357 A, G CDK2 chr12 56364792 56364793 A, G CDK2 chr12 56481333 56481334 C, G ERBB3 chr12 56481734 56481735 C, G ERBB3 chr12 56482858 56482859 A, G ERBB3 chr12 56487200 56487201 C, T ERBB3 chr12 56493821 56493822 A, C ERBB3 chr12 56494990 56494991 A, G ERBB3 chr12 56494997 56494998 A, T ERBB3 chr12 56495305 56495306 C, T ERBB3 chr12 58143087 58143088 C, T CDK4 chr12 58144780 58144781 C, T CDK4 chr12 58144920 58144921 C, G CDK4 chr12 68551930 68551931 A, G IFNG chr12 69202325 69202326 C, T MDM2 chr12 69207323 69207324 A, C MDM2 chr12 69209571 69209572 A, G MDM2 chr12 69233214 69233215 A, G MDM2 chr12 104324265 104324266 A, G HSP90B1 chr12 104325458 104325459 C, G HSP90B1 chr12 104332256 104332257 C, T HSP90B1 chr12 104335379 104335380 A, C HSP90B1 chr12 104337666 104337667 A, G HSP90B1 chr12 104340740 104340741 A, G HSP90B1 chr12 104341102 104341103 C, T HSP90B1 chr12 112856953 112856954 C, G PTPN11 chr12 112856982 112856983 A, C PTPN11 chr12 120762764 120762765 C, T PLA2G1B chr12 120762836 120762837 A, G PLA2G1B chr12 121592688 121592689 C, T P2RX7 chr12 121598651 121598652 A, G P2RX7 chr12 121598790 121598791 A, C P2RX7 chr12 121600179 121600180 C, T P2RX7 chr12 121600251 121600252 A, G P2RX7 chr12 121600252 121600253 C, T P2RX7 chr12 121603293 121603294 C, T P2RX7 chr12 121603807 121603808 A, T P2RX7 chr12 121603839 121603840 C, T P2RX7 chr12 121603855 121603856 C, G P2RX7 chr12 121605353 121605354 C, T P2RX7 chr12 121605354 121605355 A, G P2RX7 chr12 121613143 121613144 C, G P2RX7 chr12 121614933 121614934 C, T P2RX7 chr12 121615102 121615103 A, G P2RX7 chr12 121615130 121615131 C, G P2RX7 chr12 121618140 121618141 A, C P2RX7 chr12 121618234 121618235 A, G P2RX7 chr12 121618256 121618257 C, G P2RX7 chr12 121622114 121622115 C, T P2RX7 chr12 121622195 121622196 A, G P2RX7 chr12 121622238 121622239 C, T P2RX7 chr12 121622303 121622304 A, C P2RX7 chr12 121622379 121622380 C, G P2RX7 chr12 121622380 121622381 A, G P2RX7 chr12 121622418 121622419 G, T P2RX7 chr12 121622562 121622563 A, G P2RX7 chr12 122694296 122694297 C, T DIABLO chr12 122701000 122701001 A, T DIABLO chr12 125397552 125397553 C, T UBC chr12 125398038 125398039 C, G UBC chr12 125398318 125398319 A, G UBC chr12 130647708 130647709 C, G FZD10 chr12 130649133 130649134 C, T FZD10 chr12 133201326 133201327 A, T POLE chr12 133201946 133201947 C, T POLE chr12 133202003 133202004 C, T POLE chr12 133202214 133202215 A, G POLE chr12 133208978 133208979 C, T POLE chr12 133212484 133212485 C, T POLE chr12 133214694 133214695 G, T POLE chr12 133215910 133215911 C, T POLE chr12 133218209 133218210 C, G POLE chr12 133218276 133218277 A, G POLE chr12 133219830 133219831 C, T POLE chr12 133219948 133219949 A, G POLE chr12 133219988 133219989 A, T POLE chr12 133220525 133220526 C, T POLE chr12 133235999 133236000 C, T POLE chr12 133236029 133236030 C, T POLE chr12 133237686 133237687 A, G POLE chr12 133238075 133238076 C, T POLE chr12 133240966 133240967 A, G POLE chr12 133241062 133241063 C, T POLE chr12 133242048 133242049 C, T POLE chr12 133245148 133245149 A, G POLE chr12 133245546 133245547 A, G POLE chr12 133250117 133250118 C, T POLE chr12 133250196 133250197 C, T POLE chr12 133251938 133251939 A, G POLE chr12 133252692 133252693 C, T POLE chr12 133252795 133252796 C, G POLE chr12 133253194 133253195 G POLE chr12 133253994 133253995 A, G POLE chr12 133254082 133254083 C, T POLE chr12 133256697 133256698 C, T POLE chr12 133263824 133263825 A, G POLE chr13 26828915 26828916 C, T CDK8 chr13 26928054 26928055 C, T CDK8 chr13 26971194 26971195 A, G CDK8 chr13 26974561 26974562 A, G CDK8 chr13 26974573 26974574 C, T CDK8 chr13 28578208 28578209 C, G FLT3 chr13 28578212 28578213 C, T FLT3 chr13 28601172 28601173 C, T FLT3 chr13 28602255 28602256 C, T FLT3 chr13 28602291 28602292 C, T FLT3 chr13 28608282 28608283 A, G FLT3 chr13 28608458 28608459 C, T FLT3 chr13 28608472 28608473 C, T FLT3 chr13 28609650 28609651 C, G FLT3 chr13 28610044 28610045 C, T FLT3 chr13 28610182 28610183 A, G FLT3 chr13 28611381 28611382 G, T FLT3 chr13 28622355 28622356 A, G FLT3 chr13 28623698 28623699 G, T FLT3 chr13 28623758 28623759 C, T FLT3 chr13 28624293 28624294 A, G FLT3 chr13 28636083 28636084 A, G FLT3 chr13 28644585 28644586 C, T FLT3 chr13 28674557 28674558 A, G FLT3 chr13 28674627 28674628 C, T FLT3 chr13 28882947 28882948 A, G FLT1 chr13 28883060 28883061 A, G FLT1 chr13 28893641 28893642 A, G FLT1 chr13 28893687 28893688 A, G FLT1 chr13 28896978 28896979 C, T FLT1 chr13 28959076 28959077 A, G FLT1 chr13 28964197 28964198 C, T FLT1 chr13 28971023 28971024 C, T FLT1 chr13 28973172 28973173 A, G FLT1 chr13 28973312 28973313 A, G FLT1 chr13 28979993 28979994 A, G FLT1 chr13 29001429 29001430 A, G FLT1 chr13 29004324 29004325 A, C FLT1 chr13 29041006 29041007 A, T FLT1 chr13 29041580 29041581 A, C FLT1 chr13 29041592 29041593 G, T FLT1 chr13 32890571 32890572 A, G BRCA2 chr13 32900439 32900440 A, T BRCA2 chr13 32903684 32903685 C, T BRCA2 chr13 32906479 32906480 A, C BRCA2 chr13 32906728 32906729 A, C BRCA2 chr13 32906979 32906980 A, G BRCA2 chr13 32907402 32907403 C, T BRCA2 chr13 32910720 32910721 C, T BRCA2 chr13 32910841 32910842 A, G BRCA2 chr13 32911462 32911463 A, G BRCA2 chr13 32911755 32911756 C, T BRCA2 chr13 32912360 32912361 G BRCA2 chr13 32913054 32913055 A, G BRCA2 chr13 32913909 32913910 A, G BRCA2 chr13 32914195 32914196 A, G BRCA2 chr13 32914838 32914839 A, G BRCA2 chr13 32915004 32915005 C, G BRCA2 chr13 32929006 32929007 C, G BRCA2 chr13 32929231 32929232 A, G BRCA2 chr13 32929308 32929309 A, G BRCA2 chr13 32929386 32929387 C, T BRCA2 chr13 32930597 32930598 C, T BRCA2 chr13 32944666 32944667 A, C BRCA2 chr13 32953528 32953529 A, T BRCA2 chr13 32953549 32953550 A, G BRCA2 chr13 32972379 32972380 A, G BRCA2 chr13 48916861 48916862 C, T RB1 chr13 48916894 48916895 C, T RB1 chr13 48919357 48919358 G, T RB1 chr13 48919380 48919381 A, G RB1 chr13 48921922 48921923 A, G RB1 chr13 48934297 48934298 A, T RB1 chr13 48947468 48947469 G, T RB1 chr13 48955457 48955458 C, G RB1 chr13 49047416 49047417 A, G RB1 chr13 49051011 49051012 C, T RB1 chr13 49051480 49051481 A, T RB1 chr13 78473967 78473968 C, T EDNRB chr13 78475312 78475313 C, T EDNRB chr13 78477664 78477665 A, G EDNRB chr13 78477673 78477674 A, G EDNRB chr13 95097955 95097956 C, T DCT chr13 95114397 95114398 A, G DCT chr13 95117925 95117926 C, T DCT chr13 95121252 95121253 A, G DCT chr13 95121342 95121343 C DCT chr13 102375149 102375150 C, T FGF14 chr13 102379087 102379088 A, G FGF14 chr13 103460018 103460019 A, G ERCC5 chr13 103474030 103474031 C, T ERCC5 chr13 103483990 103483991 C, T ERCC5 chr13 103498542 103498543 A, G ERCC5 chr13 103498544 103498545 C, T ERCC5 chr13 103504516 103504517 C, T ERCC5 chr13 103506685 103506686 C, G ERCC5 chr13 103511300 103511301 C, T ERCC5 chr13 103513950 103513951 A, G ERCC5 chr13 103514938 103514939 C, T ERCC5 chr13 103515378 103515379 A, C ERCC5 chr13 103518161 103518162 A, C ERCC5 chr13 103524761 103524762 C, T ERCC5 chr13 103528001 103528002 C, G ERCC5 chr13 108922642 108922643 C, G TNFSF13B chr13 108955574 108955575 C, T TNFSF13B chr13 108955932 108955933 C, T TNFSF13B chr13 110408582 110408583 C, T IRS2 chr13 110435230 110435231 C, T IRS2 chr13 110435405 110435406 C, T IRS2 chr13 110435769 110435770 C, T IRS2 chr13 110435952 110435953 A, G IRS2 chr13 110436057 110436058 A, G IRS2 chr13 110436231 110436232 A, G IRS2 chr13 110436486 110436487 A, G IRS2 chr13 110436666 110436667 C, T IRS2 chr13 110436866 110436867 C, T IRS2 chr14 20811771 20811772 A, C PARP2 chr14 20811910 20811911 C, G PARP2 chr14 20813641 20813642 A, G PARP2 chr14 20813671 20813672 A, G PARP2 chr14 20814939 20814940 C, G PARP2 chr14 20815012 20815013 C, T PARP2 chr14 20819226 20819227 A, G PARP2 chr14 20822255 20822256 A, G PARP2 chr14 20822307 20822308 A, G PARP2 chr14 20823051 20823052 A, G PARP2 chr14 20823094 20823095 A, G PARP2 chr14 20824180 20824181 C, T PARP2 chr14 20824620 20824621 A, G PARP2 chr14 20824624 20824625 C, T PARP2 chr14 20824858 20824859 C, T PARP2 chr14 20824901 20824902 C, T PARP2 chr14 20825322 20825323 G, T PARP2 chr14 20942743 20942744 A, G PNP chr14 20942752 20942753 C, T PNP chr14 20942755 20942756 A, G PNP chr14 20943141 20943142 A, G PNP chr14 23504020 23504021 A, G PSMB5 chr14 23777080 23777081 A, G BCL2L2 chr14 23777098 23777099 A, G BCL2L2 chr14 23844978 23844979 A, C IL25 chr14 25042908 25042909 A, G CTSG chr14 25043670 25043671 C, T CTSG chr14 25043835 25043836 C, G CTSG chr14 25043950 25043951 A, G CTSG chr14 25045385 25045386 C, G CTSG chr14 35871216 35871217 A, G NFKBIA chr14 35871959 35871960 A, G NFKBIA chr14 35872093 35872094 C, T NFKBIA chr14 35872925 35872926 A, G NFKBIA chr14 35872988 35872989 A, G NFKBIA chr14 35873769 35873770 A, G NFKBIA chr14 36988828 36988829 A, G NKX2-1 chr14 38679001 38679002 A, G SSTR1 chr14 38679472 38679473 C, T SSTR1 chr14 62188396 62188397 C, T HIF1A chr14 62207556 62207557 C, T HIF1A chr14 62207574 62207575 A, G HIF1A chr14 62213847 62213848 C, T HIF1A chr14 64694194 64694195 C, T ESR2 chr14 64694234 64694235 C, T ESR2 chr14 64700044 64700045 C, T ESR2 chr14 64716312 64716313 C, G ESR2 chr14 64724050 64724051 C, T ESR2 chr14 64726853 64726854 A, T ESR2 chr14 64735495 64735496 A, G ESR2 chr14 64735534 64735535 A, G ESR2 chr14 64746765 64746766 A, T ESR2 chr14 64749322 64749323 G, T ESR2 chr14 64749696 64749697 C, T ESR2 chr14 75409340 75409341 C, T PGF chr14 75413010 75413011 C, T PGF chr14 75415338 75415339 G, T PGF chr14 75415999 75416000 C, T PGF chr14 81422177 81422178 A, C TSHR chr14 81534708 81534709 A, T TSHR chr14 81554262 81554263 C, T TSHR chr14 81554393 81554394 A, T TSHR chr14 81558964 81558965 A, G TSHR chr14 81562997 81562998 C, T TSHR chr14 81574815 81574816 C, G TSHR chr14 81574958 81574959 A, G TSHR chr14 81609722 81609723 A, C TSHR chr14 81609778 81609779 A, G TSHR chr14 81610633 81610634 C, G TSHR chr14 90865461 90865462 C, G CALM1 chr14 90866467 90866468 A, G CALM1 chr14 94844842 94844843 G, T SERPINA1 chr14 94847261 94847262 A, T SERPINA1 chr14 94847284 94847285 A, G SERPINA1 chr14 94847350 94847351 C, T SERPINA1 chr14 94847414 94847415 A, G SERPINA1 chr14 94849150 94849151 A, G SERPINA1 chr14 94849200 94849201 C, T SERPINA1 chr14 102548150 102548151 A, G HSP90AA1 chr14 102548440 102548441 G, T HSP90AA1 chr14 102549982 102549983 C, T HSP90AA1 chr14 102550085 102550086 A, C HSP90AA1 chr14 102551787 102551788 A, G HSP90AA1 chr14 102552489 102552490 C, T HSP90AA1 chr14 102552772 102552773 A, G HSP90AA1 chr14 102552774 102552775 G, T HSP90AA1 chr14 102568366 102568367 A, T HSP90AA1 chr14 105238669 105238670 C, T AKT1 chr14 105238782 105238783 A, G AKT1 chr14 105239435 105239436 A, G AKT1 chr14 105240226 105240227 C, G AKT1 chr14 105241303 105241304 A, G AKT1 chr14 105241377 105241378 C, T AKT1 chr14 105241398 105241399 C, T AKT1 chr14 105241421 105241422 A, G AKT1 chr14 105242965 105242966 C, T AKT1 chr14 105258891 105258892 C, T AKT1 chr14 105258892 105258893 A, G AKT1 chr15 41020860 41020861 G, T RAD51 chr15 41021050 41021051 A, T RAD51 chr15 41221986 41221987 C, T DLL4 chr15 41222024 41222025 C, T DLL4 chr15 41227148 41227149 C, T DLL4 chr15 41795739 41795740 A, G LTK chr15 41796497 41796498 A, T LTK chr15 41796598 41796599 C, T LTK chr15 41797295 41797296 C, T LTK chr15 41798216 41798217 C, T LTK chr15 41799710 41799711 C, T LTK chr15 41799847 41799848 A, G LTK chr15 41803795 41803796 G, T LTK chr15 41803806 41803807 A, G LTK chr15 41803826 41803827 C, T LTK chr15 41805114 41805115 A, G LTK chr15 41805236 41805237 C, T LTK chr15 51502843 51502844 A, C CYP19A1 chr15 51503880 51503881 A, T CYP19A1 chr15 51503896 51503897 A, G CYP19A1 chr15 51507873 51507874 A, G CYP19A1 chr15 51507967 51507968 A, G CYP19A1 chr15 51510867 51510868 A, C CYP19A1 chr15 51514571 51514572 A, G CYP19A1 chr15 51529111 51529112 C, T CYP19A1 chr15 51529165 51529166 A, G CYP19A1 chr15 51529232 51529233 A, G CYP19A1 chr15 51529264 51529265 C, T CYP19A1 chr15 51534994 51534995 A, G CYP19A1 chr15 66679797 66679798 C, G MAP2K1 chr15 66679818 66679819 C, G MAP2K1 chr15 66727596 66727597 C, G MAP2K1 chr15 66729249 66729250 C, T MAP2K1 chr15 66735550 66735551 C, T MAP2K1 chr15 66779596 66779597 A, T MAP2K1 chr15 67430336 67430337 A, G SMAD3 chr15 67457334 67457335 A, G SMAD3 chr15 67457697 67457698 A, G SMAD3 chr15 67482695 67482696 A, G SMAD3 chr15 67482696 67482697 C, T SMAD3 chr15 80259963 80259964 C, T BCL2A1 chr15 80260013 80260014 C, T BCL2A1 chr15 80263110 80263111 A, C BCL2A1 chr15 80263216 80263217 C, T BCL2A1 chr15 80263344 80263345 A, C BCL2A1 chr15 80263405 80263406 C, T BCL2A1 chr15 88476364 88476365 A, G NTRK3 chr15 88522551 88522552 A, C NTRK3 chr15 88576184 88576185 C, G NTRK3 chr15 88576214 88576215 A, G NTRK3 chr15 88669444 88669445 C, T NTRK3 chr15 88670347 88670348 C, G NTRK3 chr15 88726764 88726765 A, G NTRK3 chr15 90627615 90627616 C, T IDH2 chr15 90628536 90628537 A, G IDH2 chr15 90628590 90628591 A, G IDH2 chr15 90628593 90628594 C, T IDH2 chr15 90630629 90630630 A, G IDH2 chr15 90645664 90645665 C, T IDH2 chr15 91292916 91292917 A, G BLM chr15 91295109 91295110 C, T BLM chr15 91308511 91308512 T BLM chr15 91308513 91308514 G, T BLM chr15 91312312 91312313 A, G BLM chr15 91326098 91326099 C, T BLM chr15 91337478 91337479 A, G BLM chr15 91341598 91341599 G, T BLM chr15 91346922 91346923 A, C BLM chr15 91354504 91354505 C, T BLM chr15 91354519 91354520 C, T BLM chr15 91354520 91354521 A, G BLM chr15 99251097 99251098 A, G IGF1R chr15 99434776 99434777 C, T IGF1R chr15 99434797 99434798 A, G IGF1R chr15 99434815 99434816 A, C IGF1R chr15 99454538 99454539 A, C IGF1R chr15 99456248 99456249 C, T IGF1R chr15 99456252 99456253 C, T IGF1R chr15 99465472 99465473 C, T IGF1R chr15 99467933 99467934 A, C IGF1R chr15 99473407 99473408 A, T IGF1R chr15 99500604 99500605 C, T IGF1R chr16 1128894 1128895 A, G SSTR5 chr16 1129009 1129010 A, C SSTR5 chr16 1129022 1129023 C, T SSTR5 chr16 1129192 1129193 C, T SSTR5 chr16 1129224 1129225 C, T SSTR5 chr16 1129269 1129270 C, T SSTR5 chr16 1129350 1129351 C, T SSTR5 chr16 1129383 1129384 A, G SSTR5 chr16 1129524 1129525 A, G SSTR5 chr16 1129619 1129620 C, T SSTR5 chr16 1129865 1129866 C, T SSTR5 chr16 1129871 1129872 C, T SSTR5 chr16 1129911 1129912 A, G SSTR5 chr16 1131062 1131063 C, T SSTR5 chr16 1131174 1131175 A, C SSTR5 chr16 1131180 1131181 C, T SSTR5 chr16 2103485 2103486 G, T TSC2 chr16 2105562 2105563 C, T TSC2 chr16 2107185 2107186 A, G TSC2 chr16 2108846 2108847 G TSC2 chr16 2113071 2113072 C TSC2 chr16 2114371 2114372 C, T TSC2 chr16 2115463 2115464 C, G TSC2 chr16 2115480 2115481 C, T TSC2 chr16 2115505 2115506 C, T TSC2 chr16 2125787 2125788 C, T TSC2 chr16 2125833 2125834 C, T TSC2 chr16 2129191 2129192 C, G TSC2 chr16 2130189 2130190 C TSC2 chr16 2132378 2132379 C, T TSC2 chr16 2132512 2132513 C, G TSC2 chr16 2133639 2133640 C, G TSC2 chr16 2133725 2133726 C, T TSC2 chr16 2133726 2133727 A, G TSC2 chr16 2133797 2133798 A, G TSC2 chr16 2134437 2134438 C, T TSC2 chr16 2135070 2135071 C, T TSC2 chr16 2136865 2136866 C, T TSC2 chr16 2137856 2137857 C, T TSC2 chr16 2138217 2138218 A, C TSC2 chr16 2138218 2138219 C, T TSC2 chr16 2138268 2138269 C, T TSC2 chr16 2138397 2138398 C, T TSC2 chr16 2138421 2138422 C, G TSC2 chr16 2138507 2138508 C, G TSC2 chr16 2138583 2138584 C, G TSC2 chr16 2138636 2138637 A, G TSC2 chr16 2692463 2692464 A, G PDPK1 chr16 3293887 3293888 C, T MEFV chr16 3293895 3293896 C, T MEFV chr16 3293921 3293922 A, T MEFV chr16 3294245 3294246 A, G MEFV chr16 3296615 3296616 C, T MEFV chr16 3297072 3297073 A, G MEFV chr16 3297099 3297100 A, G MEFV chr16 3297174 3297175 C, T MEFV chr16 3297180 3297181 C, T MEFV chr16 3298946 3298947 C, G MEFV chr16 3299031 3299032 C, T MEFV chr16 3299467 3299468 C, T MEFV chr16 3299585 3299586 A, G MEFV chr16 3299748 3299749 A, G MEFV chr16 3301896 3301897 A, G MEFV chr16 3304128 3304129 C, G MEFV chr16 3304157 3304158 C, T MEFV chr16 3304462 3304463 C, T MEFV chr16 3304572 3304573 G, T MEFV chr16 3304625 3304626 C, G MEFV chr16 3304653 3304654 C, T MEFV chr16 3304734 3304735 C, T MEFV chr16 3304738 3304739 A, G MEFV chr16 3304761 3304762 A, G MEFV chr16 3778336 3778337 A, G CREBBP chr16 3779059 3779060 A, G CREBBP chr16 3779377 3779378 A, G CREBBP chr16 3781249 3781250 A, G CREBBP chr16 3781312 3781313 A, G CREBBP chr16 3794790 3794791 A, G CREBBP chr16 3795291 3795292 G, T CREBBP chr16 3795362 3795363 A, G CREBBP chr16 3817842 3817843 A, G CREBBP chr16 3819260 3819261 C, T CREBBP chr16 3820666 3820667 C, T CREBBP chr16 3824731 3824732 C, T CREBBP chr16 3827552 3827553 A, G CREBBP chr16 3831186 3831187 A, T CREBBP chr16 3832958 3832959 A, C CREBBP chr16 3860639 3860640 A, G CREBBP chr16 3929940 3929941 C, T CREBBP chr16 9916203 9916204 C, G GRIN2A chr16 9943665 9943666 C, T GRIN2A chr16 9984972 9984973 C, G GRIN2A chr16 15797842 15797843 C, G MYH11 chr16 15809116 15809117 C, T MYH11 chr16 15811022 15811023 C, T MYH11 chr16 15811061 15811062 C, T MYH11 chr16 15811130 15811131 A, G MYH11 chr16 15812095 15812096 A, G MYH11 chr16 15812308 15812309 A, G MYH11 chr16 15812990 15812991 A, C MYH11 chr16 15814920 15814921 C, T MYH11 chr16 15814936 15814937 A, G MYH11 chr16 15815350 15815351 A, G MYH11 chr16 15818140 15818141 A, C MYH11 chr16 15818652 15818653 A, G MYH11 chr16 15818841 15818842 A, G MYH11 chr16 15820862 15820863 C, T MYH11 chr16 15826383 15826384 C, T MYH11 chr16 15829418 15829419 C, T MYH11 chr16 15838939 15838940 C, G MYH11 chr16 15838970 15838971 C, G MYH11 chr16 15839033 15839034 A, G MYH11 chr16 15839102 15839103 G, T MYH11 chr16 15841772 15841773 A, G MYH11 chr16 15841829 15841830 A, G MYH11 chr16 15841838 15841839 A, G MYH11 chr16 15841861 15841862 C, T MYH11 chr16 15842004 15842005 A, G MYH11 chr16 15843957 15843958 C, T MYH11 chr16 15843964 15843965 A, G MYH11 chr16 15851654 15851655 A, G MYH11 chr16 15865471 15865472 A, G MYH11 chr16 15872747 15872748 G, T MYH11 chr16 15917226 15917227 C, T MYH11 chr16 15917320 15917321 C, T MYH11 chr16 15931974 15931975 A, G MYH11 chr16 16130356 16130357 C, T ABCC1 chr16 16130513 16130514 A, C ABCC1 chr16 16139713 16139714 C, T ABCC1 chr16 16139719 16139720 A, G ABCC1 chr16 16139877 16139878 A, G ABCC1 chr16 16146575 16146576 C, G ABCC1 chr16 16161975 16161976 A, G ABCC1 chr16 16162018 16162019 C, T ABCC1 chr16 16162038 16162039 C, T ABCC1 chr16 16173226 16173227 C, T ABCC1 chr16 16177201 16177202 A, C ABCC1 chr16 16177274 16177275 A, G ABCC1 chr16 16196493 16196494 C, T ABCC1 chr16 16200755 16200756 C, T ABCC1 chr16 16208682 16208683 C, G ABCC1 chr16 16208947 16208948 C, G ABCC1 chr16 16219728 16219729 C, T ABCC1 chr16 16225804 16225805 C ABCC1 chr16 16228241 16228242 A, G ABCC1 chr16 16232379 16232380 C, T ABCC1 chr16 16244128 16244129 C, T ABCC6 chr16 16244662 16244663 C, T ABCC6 chr16 16248679 16248680 C, T ABCC6 chr16 16248680 16248681 A, G ABCC6 chr16 16251530 16251531 C, T ABCC6 chr16 16251598 16251599 C, T ABCC6 chr16 16253291 16253292 C, G ABCC6 chr16 16255436 16255437 A, G ABCC6 chr16 16259595 16259596 A, G ABCC6 chr16 16263662 16263663 A, G ABCC6 chr16 16267220 16267221 C, G ABCC6 chr16 16271356 16271357 C, T ABCC6 chr16 16271408 16271409 A, G ABCC6 chr16 16272669 16272670 C, T ABCC6 chr16 16276291 16276292 C, T ABCC6 chr16 16276340 16276341 A, T ABCC6 chr16 16278862 16278863 G, T ABCC6 chr16 16278868 16278869 C, G ABCC6 chr16 16281006 16281007 A, G ABCC6 chr16 16281153 16281154 A, C ABCC6 chr16 16284264 16284265 C, T ABCC6 chr16 16284271 16284272 C, T ABCC6 chr16 16291857 16291858 C, G ABCC6 chr16 16291870 16291871 C, G ABCC6 chr16 16291970 16291971 C, T ABCC6 chr16 16295956 16295957 C, T ABCC6 chr16 16306058 16306059 C, T ABCC6 chr16 23646941 23646942 C, T PALB2 chr16 23647237 23647238 A, G PALB2 chr16 23690252 23690253 C, T PLK1 chr16 23691415 23691416 A, G PLK1 chr16 23691589 23691590 A, G PLK1 chr16 23692203 23692204 T PLK1 chr16 23699916 23699917 C, G PLK1 chr16 23700058 23700059 C, T PLK1 chr16 23701254 23701255 A, G PLK1 chr16 23701457 23701458 A, G PLK1 chr16 23701537 23701538 A, G PLK1 chr16 23847574 23847575 A, C PRKCB chr16 23848761 23848762 A, G PRKCB chr16 23999927 23999928 G, T PRKCB chr16 24104187 24104188 C, T PRKCB chr16 24105668 24105669 A, G PRKCB chr16 24166129 24166130 C, T PRKCB chr16 24192106 24192107 A, G PRKCB chr16 24202457 24202458 C, T PRKCB chr16 27352591 27352592 A, G IL4R chr16 27353588 27353589 C, G IL4R chr16 27356223 27356224 A, G IL4R chr16 27356270 27356271 C, T IL4R chr16 27357926 27357927 C, T IL4R chr16 27363900 27363901 A, G IL4R chr16 27367225 27367226 C, G IL4R chr16 27367259 27367260 C, T IL4R chr16 27367278 27367279 A, G IL4R chr16 27370164 27370165 A, G IL4R chr16 27373557 27373558 A, C IL4R chr16 27373611 27373612 C, T IL4R chr16 27373871 27373872 A, C IL4R chr16 27373914 27373915 G, T IL4R chr16 27373965 27373966 C, T IL4R chr16 27373971 27373972 C, T IL4R chr16 27374146 27374147 A, G IL4R chr16 27374179 27374180 C, T IL4R chr16 27374399 27374400 A, G IL4R chr16 27374407 27374408 A, G IL4R chr16 27374926 27374927 G, T IL4R chr16 27375024 27375025 C, T IL4R chr16 27375069 27375070 C, T IL4R chr16 27414440 27414441 C, T IL21R chr16 27414523 27414524 C, T IL21R chr16 27414535 27414536 C, T IL21R chr16 27441282 27441283 A, G IL21R chr16 27455885 27455886 A, G IL21R chr16 27457264 27457265 C, T IL21R chr16 27460436 27460437 A, G IL21R chr16 28944281 28944282 C, T CD19 chr16 28944395 28944396 C, G CD19 chr16 28944699 28944700 G, T CD19 chr16 28950050 28950051 A, G CD19 chr16 30128433 30128434 A, G MAPK3 chr16 31102588 31102589 A, G VKORC1 chr16 31105553 31105554 A, C VKORC1 chr16 31106014 31106015 C, T VKORC1 chr16 31273128 31273129 C, T ITGAM chr16 31283163 31283164 A, G ITGAM chr16 31289395 31289396 C, T ITGAM chr16 31308990 31308991 A, C ITGAM chr16 31332654 31332655 C, T ITGAM chr16 31332889 31332890 C, T ITGAM chr16 31335905 31335906 C, T ITGAM chr16 31336718 31336719 A, G ITGAM chr16 31336887 31336888 C, T ITGAM chr16 31340509 31340510 C, T ITGAM chr16 31340519 31340520 C, T ITGAM chr16 31343004 31343005 C, T ITGAM chr16 50733742 50733743 A, G NOD2 chr16 50733858 50733859 C, G NOD2 chr16 50741762 50741763 C, T NOD2 chr16 50744623 50744624 C, T NOD2 chr16 50745198 50745199 C, T NOD2 chr16 50745274 50745275 C, T NOD2 chr16 50745582 50745583 G, T NOD2 chr16 50745925 50745926 C, T NOD2 chr16 50745944 50745945 A, G NOD2 chr16 50745995 50745996 C, G NOD2 chr16 50746190 50746191 A, G NOD2 chr16 50750759 50750760 C, T NOD2 chr16 50750790 50750791 G NOD2 chr16 50757275 50757276 A, G NOD2 chr16 55515759 55515760 A, G MMP2 chr16 55515825 55515826 A, C MMP2 chr16 55517898 55517899 A, G MMP2 chr16 55519534 55519535 C, G MMP2 chr16 55519606 55519607 C, T MMP2 chr16 55522415 55522416 C, T MMP2 chr16 55523621 55523622 C, T MMP2 chr16 55523653 55523654 C, T MMP2 chr16 55523704 55523705 C, T MMP2 chr16 55525758 55525759 A, G MMP2 chr16 55527112 55527113 A, G MMP2 chr16 55530999 55531000 C, T MMP2 chr16 55536686 55536687 A, G MMP2 chr16 55536726 55536727 C, T MMP2 chr16 55536762 55536763 C, G MMP2 chr16 55536781 55536782 C, G MMP2 chr16 55539190 55539191 C, G MMP2 chr16 55725893 55725894 C, G SLC6A2 chr16 55725974 55725975 A, G SLC6A2 chr16 55728080 55728081 G, T SLC6A2 chr16 55729189 55729190 A, G SLC6A2 chr16 55730095 55730096 A, G SLC6A2 chr16 55730123 55730124 A, C SLC6A2 chr16 55731834 55731835 A, G SLC6A2 chr16 55731945 55731946 A, G SLC6A2 chr16 55733588 55733589 C, T SLC6A2 chr16 55734105 55734106 C, T SLC6A2 chr16 55735911 55735912 C, T SLC6A2 chr16 55739091 55739092 A, T SLC6A2 chr16 55739233 55739234 C, T SLC6A2 chr16 56792438 56792439 A, T NUP93 chr16 56852643 56852644 A, G NUP93 chr16 56863026 56863027 A, G NUP93 chr16 56864397 56864398 C, T NUP93 chr16 56864398 56864399 C, T NUP93 chr16 56865704 56865705 G, T NUP93 chr16 56868308 56868309 C, T NUP93 chr16 56868699 56868700 A, G NUP93 chr16 56868732 56868733 G NUP93 chr16 56873494 56873495 C, T NUP93 chr16 56878548 56878549 A, G NUP93 chr16 57467935 57467936 A, T CIAPIN1 chr16 57467980 57467981 A, G CIAPIN1 chr16 57468109 57468110 A, G CIAPIN1 chr16 57470563 57470564 C, G CIAPIN1 chr16 57474667 57474668 A, G CIAPIN1 chr16 57474686 57474687 C, G CIAPIN1 chr16 66420884 66420885 C, T CDH5 chr16 66422317 66422318 A, G CDH5 chr16 66430136 66430137 G, T CDH5 chr16 66432380 66432381 C, T CDH5 chr16 66432422 66432423 C, T CDH5 chr16 66432423 66432424 C, T CDH5 chr16 66847574 66847575 C, T NAE1 chr16 66847657 66847658 A, T NAE1 chr16 66850763 66850764 C, G NAE1 chr16 66851223 66851224 C, T NAE1 chr16 66857572 66857573 C, G NAE1 chr16 66861965 66861966 A, G NAE1 chr16 66864713 66864714 G, T NAE1 chr16 67063611 67063612 G, T CBFB chr16 67116168 67116169 C, T CBFB chr16 67663290 67663291 C, T CTCF chr16 68771370 68771371 C, G CDH1 chr16 68771371 68771372 C, T CDH1 chr16 68842479 68842480 C, G CDH1 chr16 68847442 68847443 C, G CDH1 chr16 68856040 68856041 A, G CDH1 chr16 68856087 68856088 C, T CDH1 chr16 68857440 68857441 C, T CDH1 chr16 69745144 69745145 A, G NQO1 chr16 69748927 69748928 C, G NQO1 chr16 69752372 69752373 C, T NQO1 chr16 69760260 69760261 G, T NQO1 chr16 69760285 69760286 C, G NQO1 chr16 69760340 69760341 A, G NQO1 chr16 71674881 71674882 C, G PHLPP2 chr16 71674954 71674955 C, T PHLPP2 chr16 71678662 71678663 C, T PHLPP2 chr16 71678761 71678762 C, G PHLPP2 chr16 71682920 71682921 C, T PHLPP2 chr16 71683717 71683718 A, G PHLPP2 chr16 71692546 71692547 A, C PHLPP2 chr16 71703251 71703252 A, G PHLPP2 chr16 71710427 71710428 A, G PHLPP2 chr16 71712785 71712786 A, G PHLPP2 chr16 71718365 71718366 C, T PHLPP2 chr16 71718423 71718424 A, G PHLPP2 chr16 88709711 88709712 A, G CYBA chr16 88709827 88709828 A, G CYBA chr16 88713212 88713213 C, G CYBA chr16 88713235 88713236 A, G CYBA chr16 88713500 88713501 A, G CYBA chr16 89574833 89574834 G, T SPG7 chr16 89577045 89577046 C, T SPG7 chr16 89590242 89590243 A, G SPG7 chr16 89597056 89597057 G, T SPG7 chr16 89597109 89597110 A, G SPG7 chr16 89603355 89603356 G, T SPG7 chr16 89613122 89613123 A, G SPG7 chr16 89615465 89615466 C, T SPG7 chr16 89615541 89615542 G SPG7 chr16 89615764 89615765 G, T SPG7 chr16 89616886 89616887 A, C SPG7 chr16 89619554 89619555 C, T SPG7 chr16 89620147 89620148 A, G SPG7 chr16 89620157 89620158 A, G SPG7 chr16 89620185 89620186 C, G SPG7 chr16 89620301 89620302 A, G SPG7 chr16 89623300 89623301 A, G SPG7 chr16 89623407 89623408 C, T SPG7 chr16 89805260 89805261 A, G FANCA chr16 89805671 89805672 C, T FANCA chr16 89805913 89805914 C, T FANCA chr16 89805969 89805970 C, T FANCA chr16 89805976 89805977 A, G FANCA chr16 89806062 89806063 C, G FANCA chr16 89806342 89806343 A, C FANCA chr16 89806346 89806347 A, T FANCA chr16 89806476 89806477 C, T FANCA chr16 89807232 89807233 C, G FANCA chr16 89809170 89809171 C, T FANCA chr16 89809318 89809319 C, T FANCA chr16 89813193 89813194 C, T FANCA chr16 89813205 89813206 A, G FANCA chr16 89815048 89815049 C, T FANCA chr16 89815151 89815152 A, G FANCA chr16 89816313 89816314 A, G FANCA chr16 89816332 89816333 C, T FANCA chr16 89825064 89825065 A, G FANCA chr16 89828436 89828437 A, G FANCA chr16 89831492 89831493 C, G FANCA chr16 89831509 89831510 A, C FANCA chr16 89831519 89831520 A, T FANCA chr16 89836322 89836323 C, T FANCA chr16 89836508 89836509 C, G FANCA chr16 89836550 89836551 A, G FANCA chr16 89837137 89837138 G, T FANCA chr16 89838077 89838078 A, G FANCA chr16 89838085 89838086 A, C FANCA chr16 89839751 89839752 C, T FANCA chr16 89839765 89839766 C, G FANCA chr16 89839853 89839854 C, T FANCA chr16 89845193 89845194 A, G FANCA chr16 89845286 89845287 A, G FANCA chr16 89846396 89846397 A, G FANCA chr16 89849479 89849480 C, T FANCA chr16 89857879 89857880 C, T FANCA chr16 89858416 89858417 A, C FANCA chr16 89858504 89858505 C, T FANCA chr16 89858524 89858525 C, G FANCA chr16 89862416 89862417 C FANCA chr16 89862433 89862434 C, T FANCA chr16 89866042 89866043 C, T FANCA chr16 89869703 89869704 C, T FANCA chr16 89869760 89869761 C, T FANCA chr16 89874755 89874756 A, G FANCA chr16 89877234 89877235 A, T FANCA chr16 89877268 89877269 C, T FANCA chr16 89882358 89882359 G, T FANCA chr16 89882999 89883000 C, G FANCA chr16 89883006 89883007 A, T FANCA chr17 6902178 6902179 A, G ALOX12 chr17 6902294 6902295 A, G ALOX12 chr17 6902742 6902743 A, G ALOX12 chr17 6902759 6902760 A, G ALOX12 chr17 6909837 6909838 A, G ALOX12 chr17 6913651 6913652 A, G ALOX12 chr17 7462554 7462555 A, G TNFSF13 chr17 7462580 7462581 C, G TNFSF13 chr17 7462968 7462969 A, G TNFSF13 chr17 7464218 7464219 C, T TNFSF13 chr17 7579471 7579472 C, G TP53 chr17 7579547 7579548 A, G TP53 chr17 7579595 7579596 A, G TP53 chr17 7579800 7579801 C, G TP53 chr17 7976916 7976917 A, T ALOX12B chr17 7979451 7979452 G, T ALOX12B chr17 7979462 7979463 A, G ALOX12B chr17 7983680 7983681 A, G ALOX12B chr17 7984156 7984157 A, C ALOX12B chr17 7989405 7989406 C, T ALOX12B chr17 7990718 7990719 A, G ALOX12B chr17 8108330 8108331 A, G AURKB chr17 8108338 8108339 A, G AURKB chr17 8109964 8109965 A, G AURKB chr17 8109992 8109993 A, G AURKB chr17 8110939 8110940 A, G AURKB chr17 9729444 9729445 A, T GLP2R chr17 9739700 9739701 C, T GLP2R chr17 9745902 9745903 A, G GLP2R chr17 9760715 9760716 G, T GLP2R chr17 9763474 9763475 C, T GLP2R chr17 9764530 9764531 A, G GLP2R chr17 9764546 9764547 C, G, T GLP2R chr17 9769059 9769060 A, T GLP2R chr17 9769061 9769062 A, T GLP2R chr17 9769198 9769199 C, T GLP2R chr17 9773983 9773984 C, G GLP2R chr17 9774056 9774057 G, T GLP2R chr17 9791158 9791159 A, G GLP2R chr17 9792767 9792768 A, G GLP2R chr17 9792773 9792774 C, T GLP2R chr17 9792871 9792872 C, T GLP2R chr17 9792927 9792928 A, G GLP2R chr17 9793416 9793417 A, T GLP2R chr17 12043293 12043294 C, T MAP2K4 chr17 15134320 15134321 A, G PMP22 chr17 15142754 15142755 A, G PMP22 chr17 16285929 16285930 C, T UBB chr17 29486151 29486152 A, G NF1 chr17 29508774 29508775 A, G NF1 chr17 29508882 29508883 A NF1 chr17 29528561 29528562 A, G NF1 chr17 29546174 29546175 C, T NF1 chr17 29550597 29550598 A, T NF1 chr17 29552199 29552200 A, G NF1 chr17 29553472 29553473 C, T NF1 chr17 29553484 29553485 A, G NF1 chr17 29554201 29554202 C, T NF1 chr17 29559917 29559918 T NF1 chr17 29559931 29559932 A, C NF1 chr17 29559941 29559942 A, C NF1 chr17 29562904 29562905 A, G NF1 chr17 29592392 29592393 C, T NF1 chr17 29652883 29652884 C, T NF1 chr17 29652930 29652931 A, G NF1 chr17 29653036 29653037 A, G NF1 chr17 29653292 29653293 C, T NF1 chr17 29677183 29677184 C, T NF1 chr17 29679245 29679246 A, G NF1 chr17 29683993 29683994 C, T NF1 chr17 29685688 29685689 C, T NF1 chr17 29694380 29694381 C, T NF1 chr17 29705946 29705947 C, T NF1 chr17 33433202 33433203 C, T RAD51L3 chr17 33445548 33445549 A, G RAD51L3 chr17 33446669 33446670 A, C RAD51L3 chr17 34416150 34416151 A, C CCL3 chr17 34416664 34416665 A, G CCL3 chr17 34417291 34417292 A, G CCL3 chr17 34417308 34417309 C, G CCL3 chr17 37561612 37561613 A, G MED1 chr17 37580083 37580084 A, G MED1 chr17 37581029 37581030 C, T MED1 chr17 37603994 37603995 G, T MED1 chr17 37618594 37618595 C, T CDK12 chr17 37619037 37619038 A, G CDK12 chr17 37682090 37682091 A, G CDK12 chr17 37682199 37682200 A, G CDK12 chr17 37682291 37682292 A, G CDK12 chr17 37682374 37682375 A, T CDK12 chr17 37855833 37855834 A, C ERBB2 chr17 37856588 37856589 A, G ERBB2 chr17 37863267 37863268 A, G ERBB2 chr17 37864728 37864729 C, G ERBB2 chr17 37866004 37866005 C, T ERBB2 chr17 37866740 37866741 G, T ERBB2 chr17 37868347 37868348 C, T ERBB2 chr17 37872004 37872005 G, T ERBB2 chr17 37872034 37872035 G, T ERBB2 chr17 37872049 37872050 A, G ERBB2 chr17 37879587 37879588 A, G ERBB2 chr17 37884036 37884037 C, G ERBB2 chr17 38512822 38512823 G RARA chr17 38545823 38545824 A, C TOP2A chr17 38547867 38547868 C, T TOP2A chr17 38547908 38547909 A, G TOP2A chr17 38555205 38555206 A, G TOP2A chr17 38556532 38556533 C, T TOP2A chr17 38556769 38556770 C, T TOP2A chr17 38560394 38560395 C, T TOP2A chr17 40469125 40469126 A, G STAT3 chr17 40469179 40469180 A, G STAT3 chr17 40475055 40475056 A, G STAT3 chr17 40475382 40475383 C, G STAT3 chr17 40476945 40476946 A, T STAT3 chr17 40477063 40477064 C, G STAT3 chr17 40481528 40481529 C, G STAT3 chr17 40483465 40483466 A, C STAT3 chr17 41197828 41197829 G, T BRCA1 chr17 41222974 41222975 C, T BRCA1 chr17 41223093 41223094 C, T BRCA1 chr17 41234469 41234470 A, G BRCA1 chr17 41243999 41244000 C, T BRCA1 chr17 41244129 41244130 C, T BRCA1 chr17 41244428 41244429 C, T BRCA1 chr17 41244434 41244435 C, T BRCA1 chr17 41244935 41244936 A, G BRCA1 chr17 41244981 41244982 A, G BRCA1 chr17 41245089 41245090 C, T BRCA1 chr17 41245236 41245237 A, G BRCA1 chr17 41245465 41245466 A, G BRCA1 chr17 41245470 41245471 C, T BRCA1 chr17 41245576 41245577 C, T BRCA1 chr17 41246480 41246481 C, T BRCA1 chr17 41251930 41251931 A, G BRCA1 chr17 41258449 41258450 A, T BRCA1 chr17 41267762 41267763 C, T BRCA1 chr17 41607596 41607597 C, T ETV4 chr17 41611331 41611332 C, G ETV4 chr17 41622397 41622398 A, G ETV4 chr17 42635964 42635965 C, T FZD2 chr17 42636441 42636442 A, C FZD2 chr17 45331266 45331267 A, G ITGB3 chr17 45331283 45331284 G, T ITGB3 chr17 45331284 45331285 C, T ITGB3 chr17 45331357 45331358 C, G ITGB3 chr17 45331396 45331397 A, G ITGB3 chr17 45360679 45360680 C, T ITGB3 chr17 45360729 45360730 C, T ITGB3 chr17 45361778 45361779 A, G ITGB3 chr17 45364539 45364540 C, T ITGB3 chr17 45366990 45366991 A, G ITGB3 chr17 45367510 45367511 C, T ITGB3 chr17 45368336 45368337 A, C ITGB3 chr17 45384909 45384910 C, T ITGB3 chr17 45385011 45385012 C, T ITGB3 chr17 47685199 47685200 C, G SPOP chr17 47698019 47698020 G, T SPOP chr17 56432375 56432376 A, G RNF43 chr17 56434875 56434876 C RNF43 chr17 56435079 56435080 C, G RNF43 chr17 56435166 56435167 C, G RNF43 chr17 56435551 56435552 A, G RNF43 chr17 56436108 56436109 C, T RNF43 chr17 56439929 56439930 C, T RNF43 chr17 56440605 56440606 A, G RNF43 chr17 56448296 56448297 C, T RNF43 chr17 56492799 56492800 C, T RNF43 chr17 61557199 61557200 C, T ACE chr17 61557772 61557773 A, G ACE chr17 61557821 61557822 C, T ACE chr17 61557822 61557823 G, T ACE chr17 61557938 61557939 C, T ACE chr17 61558397 61558398 A, G ACE chr17 61558950 61558951 C, T ACE chr17 61559818 61559819 C, T ACE chr17 61559922 61559923 C, T ACE chr17 61560048 61560049 C, G ACE chr17 61560762 61560763 C, T ACE chr17 61561755 61561756 A, G ACE chr17 61562308 61562309 C, T ACE chr17 61562321 61562322 C, T ACE chr17 61562372 61562373 A, G ACE chr17 61562773 61562774 C, T ACE chr17 61564051 61564052 A, G ACE chr17 61564280 61564281 C, T ACE chr17 61565989 61565990 C, G ACE chr17 61565997 61565998 A, C ACE chr17 61566030 61566031 A, G ACE chr17 61566084 61566085 A, G ACE chr17 61568616 61568617 C, T ACE chr17 61568620 61568621 C, T ACE chr17 61571835 61571836 C, T ACE chr17 61573760 61573761 C, T ACE chr17 61574661 61574662 A, C ACE chr17 61574674 61574675 A, G ACE chr17 62007497 62007498 A, G CD79B chr17 62007776 62007777 A, G CD79B chr17 62496669 62496670 A, C DDX5 chr17 62499700 62499701 C, G DDX5 chr17 62500752 62500753 C, T DDX5 chr17 63049708 63049709 C, T GNA13 chr17 63049823 63049824 A, C GNA13 chr17 64685077 64685078 A, G PRKCA chr17 64737716 64737717 A, T PRKCA chr17 64737762 64737763 A, G PRKCA chr17 64784938 64784939 C, T PRKCA chr17 64785021 64785022 A, G PRKCA chr17 66511626 66511627 A, G PRKAR1A chr17 66519971 66519972 C, T PRKAR1A chr17 66520243 66520244 C, T PRKAR1A chr17 66521876 66521877 A, G PRKAR1A chr17 66524986 66524987 A, G PRKAR1A chr17 66526026 66526027 G, T PRKAR1A chr17 71166700 71166701 A, G SSTR2 chr17 76210366 76210367 C, G BIRC5 chr17 76218868 76218869 A, G BIRC5 chr17 76219522 76219523 A, G BIRC5 chr17 76219590 76219591 A, G BIRC5 chr17 76219610 76219611 C, T BIRC5 chr17 78519518 78519519 C, T RPTOR chr17 78599468 78599469 G, T RPTOR chr17 78599561 78599562 C, G RPTOR chr17 78617438 78617439 C, T RPTOR chr17 78681589 78681590 A, G RPTOR chr17 78727791 78727792 A, G RPTOR chr17 78811769 78811770 A, G RPTOR chr17 78820328 78820329 C, T RPTOR chr17 78820373 78820374 A, G RPTOR chr17 78829174 78829175 A, G RPTOR chr17 78854222 78854223 A, G RPTOR chr17 78858815 78858816 C, T RPTOR chr17 78865545 78865546 C, T RPTOR chr17 78865629 78865630 A, G RPTOR chr17 78896528 78896529 C, T RPTOR chr17 78921107 78921108 A, G RPTOR chr17 78921116 78921117 C, T RPTOR chr17 78923177 78923178 C, T RPTOR chr17 78931413 78931414 A, G RPTOR chr17 78934033 78934034 C, G RPTOR chr17 78935196 78935197 C, T RPTOR chr17 78936702 78936703 C, G RPTOR chr17 78936704 78936705 C, T RPTOR chr18 658000 658001 A, G TYMS chr18 662134 662135 A, G TYMS chr18 662246 662247 A, G TYMS chr18 662369 662370 C, T TYMS chr18 669186 669187 C, T TYMS chr18 671519 671520 C, T TYMS chr18 673015 673016 C, T TYMS chr18 724611 724612 A, G YES1 chr18 732811 732812 C, G YES1 chr18 742890 742891 A, T YES1 chr18 743435 743436 C, T YES1 chr18 745883 745884 A, C YES1 chr18 745932 745933 C, T YES1 chr18 25532303 25532304 C, T CDH2 chr18 25543386 25543387 A, G CDH2 chr18 25565081 25565082 A, G CDH2 chr18 25572836 25572837 A, G CDH2 chr18 25572848 25572849 C, T CDH2 chr18 25583095 25583096 A, G CDH2 chr18 25589674 25589675 A, T CDH2 chr18 25589686 25589687 C CDH2 chr18 25616450 25616451 A, T CDH2 chr18 25727747 25727748 C, T CDH2 chr18 45371685 45371686 C, T SMAD2 chr18 45371694 45371695 A, G SMAD2 chr18 45375014 45375015 C, T SMAD2 chr18 48577781 48577782 C, G SMAD4 chr18 48586183 48586184 A, G SMAD4 chr18 48586343 48586344 C, T SMAD4 chr18 59157763 59157764 C, T CDH20 chr18 59157902 59157903 A, G CDH20 chr18 59166387 59166388 A, G CDH20 chr18 59166522 59166523 C, T CDH20 chr18 59166540 59166541 C, T CDH20 chr18 59167580 59167581 G, T CDH20 chr18 59174601 59174602 A, G CDH20 chr18 59174758 59174759 A, C CDH20 chr18 59195352 59195353 C CDH20 chr18 59195353 59195354 C, T CDH20 chr18 59203706 59203707 A, G CDH20 chr18 59212413 59212414 A, T CDH20 chr18 59217171 59217172 C, T CDH20 chr18 59221549 59221550 A, G CDH20 chr18 60985603 60985604 C, T BCL2 chr18 60985609 60985610 A, G BCL2 chr18 60985618 60985619 G, T BCL2 chr18 60985621 60985622 A, G BCL2 chr18 60985772 60985773 C, T BCL2 chr18 60985878 60985879 C, T BCL2 chr18 61066462 61066463 A, G VPS4B chr18 61067817 61067818 A, G VPS4B chr18 61067958 61067959 C, T VPS4B chr18 61077632 61077633 A, G VPS4B chr19 1000419 1000420 A, G GRIN3B chr19 1000716 1000717 A, C GRIN3B chr19 1000784 1000785 C, T GRIN3B chr19 1000798 1000799 C, G GRIN3B chr19 1003136 1003137 C, T GRIN3B chr19 1003157 1003158 C, T GRIN3B chr19 1003161 1003162 C, T GRIN3B chr19 1003171 1003172 C, T GRIN3B chr19 1003220 1003221 A, C GRIN3B chr19 1003373 1003374 A, G GRIN3B chr19 1003438 1003439 A, G GRIN3B chr19 1003656 1003657 A, G GRIN3B chr19 1004686 1004687 C, T GRIN3B chr19 1004708 1004709 A, G GRIN3B chr19 1004709 1004710 C, T GRIN3B chr19 1004723 1004724 A, G GRIN3B chr19 1004739 1004740 C, T GRIN3B chr19 1004807 1004808 C, T GRIN3B chr19 1004822 1004823 A, G GRIN3B chr19 1004843 1004844 C, T GRIN3B chr19 1004871 1004872 A, G GRIN3B chr19 1004882 1004883 C, T GRIN3B chr19 1005065 1005066 C GRIN3B chr19 1005185 1005186 A, G GRIN3B chr19 1005223 1005224 A, G GRIN3B chr19 1005229 1005230 C, T GRIN3B chr19 1005333 1005334 A, G GRIN3B chr19 1005426 1005427 C, T GRIN3B chr19 1005530 1005531 C, G GRIN3B chr19 1008215 1008216 A, G GRIN3B chr19 1008703 1008704 A, G GRIN3B chr19 1008744 1008745 A, G GRIN3B chr19 1008878 1008879 C, G GRIN3B chr19 1009188 1009189 A, G GRIN3B chr19 1009364 1009365 A, T GRIN3B chr19 1009484 1009485 C, G GRIN3B chr19 1009526 1009527 C, T GRIN3B chr19 1207175 1207176 A, C STK11 chr19 1218383 1218384 C, T STK11 chr19 1219273 1219274 A, G STK11 chr19 1221160 1221161 C, T STK11 chr19 1221292 1221293 C, T STK11 chr19 1222011 1222012 C, G STK11 chr19 1223124 1223125 C, G STK11 chr19 2164350 2164351 A, T DOT1L chr19 2199813 2199814 C, T DOT1L chr19 2202789 2202790 A, T DOT1L chr19 2208858 2208859 C, T DOT1L chr19 2211220 2211221 C, T DOT1L chr19 2213523 2213524 C, T DOT1L chr19 2213894 2213895 A, G DOT1L chr19 2216918 2216919 C, T DOT1L chr19 2222470 2222471 A, T DOT1L chr19 2223274 2223275 C, T DOT1L chr19 2223326 2223327 A, G DOT1L chr19 2226675 2226676 A, G DOT1L chr19 2226771 2226772 C, G DOT1L chr19 2226854 2226855 C, T DOT1L chr19 2226876 2226877 A, G DOT1L chr19 2227129 2227130 C, G DOT1L chr19 2227140 2227141 C, T DOT1L chr19 2229692 2229693 A, G DOT1L chr19 3110348 3110349 G, T GNA11 chr19 3110360 3110361 C, T GNA11 chr19 3119238 3119239 C, T GNA11 chr19 3119364 3119365 C, G GNA11 chr19 3119404 3119405 G, T GNA11 chr19 3119405 3119406 G, T GNA11 chr19 3976704 3976705 C, T EEF2 chr19 3976759 3976760 A, G EEF2 chr19 3977470 3977471 A, G EEF2 chr19 3977485 3977486 A, G EEF2 chr19 3977500 3977501 C, T EEF2 chr19 3978193 3978194 C, T EEF2 chr19 3979407 3979408 A, G EEF2 chr19 3979469 3979470 C, T EEF2 chr19 3979841 3979842 C, T EEF2 chr19 3980823 3980824 A, G EEF2 chr19 3981441 3981442 A, G EEF2 chr19 3982080 3982081 T EEF2 chr19 3982323 3982324 A, G EEF2 chr19 3982784 3982785 C, T EEF2 chr19 3982791 3982792 C, G EEF2 chr19 3982849 3982850 A, G EEF2 chr19 3982930 3982931 A, G EEF2 chr19 3982966 3982967 A, G EEF2 chr19 3983081 3983082 A, G EEF2 chr19 3983183 3983184 A, G EEF2 chr19 3983301 3983302 A, G EEF2 chr19 4101195 4101196 A, G MAP2K2 chr19 4102353 4102354 C, T MAP2K2 chr19 4102448 4102449 A, G MAP2K2 chr19 4110551 4110552 C, G MAP2K2 chr19 4117527 4117528 A, G MAP2K2 chr19 6586267 6586268 A, G CD70 chr19 7125518 7125519 A, G INSR chr19 7128822 7128823 C, T INSR chr19 7132135 7132136 C, T INSR chr19 7141726 7141727 A, G INSR chr19 7141774 7141775 A, G INSR chr19 7141870 7141871 C, G INSR chr19 7142920 7142921 C, T INSR chr19 7142998 7142999 C, T INSR chr19 7150490 7150491 A, G INSR chr19 7163082 7163083 C, T INSR chr19 7163139 7163140 G, T INSR chr19 7163153 7163154 A, G INSR chr19 7163213 7163214 C, T INSR chr19 7163229 7163230 C, T INSR chr19 7166137 7166138 A, G INSR chr19 7166387 7166388 A, G INSR chr19 7184391 7184392 C, T INSR chr19 7184430 7184431 G INSR chr19 7184517 7184518 A, G INSR chr19 7267745 7267746 A, G INSR chr19 10599964 10599965 A, G KEAP1 chr19 10600441 10600442 C, G KEAP1 chr19 10600538 10600539 C, T KEAP1 chr19 10610235 10610236 A, G KEAP1 chr19 10679239 10679240 C, G CDKN2D chr19 11097708 11097709 C, T SMARCA4 chr19 11098396 11098397 A, G SMARCA4 chr19 11098411 11098412 A, C SMARCA4 chr19 11105607 11105608 C, T SMARCA4 chr19 11105864 11105865 C, G SMARCA4 chr19 11106599 11106600 C, T SMARCA4 chr19 11107084 11107085 A, G SMARCA4 chr19 11107132 11107133 C, T SMARCA4 chr19 11107133 11107134 A, G SMARCA4 chr19 11118558 11118559 T SMARCA4 chr19 11123737 11123738 C, T SMARCA4 chr19 11129599 11129600 C, T SMARCA4 chr19 11136214 11136215 C, G SMARCA4 chr19 11145690 11145691 C, T SMARCA4 chr19 11152083 11152084 G SMARCA4 chr19 11169068 11169069 A, G SMARCA4 chr19 11169513 11169514 C, T SMARCA4 chr19 11169576 11169577 A, G SMARCA4 chr19 11170695 11170696 A, G SMARCA4 chr19 11170838 11170839 C, T SMARCA4 chr19 15271449 15271450 A, T NOTCH3 chr19 15271468 15271469 C NOTCH3 chr19 15271625 15271626 A, G NOTCH3 chr19 15271685 15271686 A, G NOTCH3 chr19 15271770 15271771 A, G NOTCH3 chr19 15272000 15272001 C, T NOTCH3 chr19 15272336 15272337 A, G NOTCH3 chr19 15273380 15273381 A, G NOTCH3 chr19 15273423 15273424 C, T NOTCH3 chr19 15276142 15276143 C, T NOTCH3 chr19 15276738 15276739 A, G NOTCH3 chr19 15276918 15276919 A, G NOTCH3 chr19 15278056 15278057 A, G NOTCH3 chr19 15281385 15281386 A, C NOTCH3 chr19 15281458 15281459 C, G NOTCH3 chr19 15285051 15285052 C, T NOTCH3 chr19 15288694 15288695 A, G NOTCH3 chr19 15289822 15289823 A, C NOTCH3 chr19 15290006 15290007 C, T NOTCH3 chr19 15290124 15290125 A, G NOTCH3 chr19 15291095 15291096 A, G NOTCH3 chr19 15291575 15291576 C, G NOTCH3 chr19 15291698 15291699 C, T NOTCH3 chr19 15291714 15291715 C, T NOTCH3 chr19 15292436 15292437 C, T NOTCH3 chr19 15295133 15295134 A, G NOTCH3 chr19 15296402 15296403 C, T NOTCH3 chr19 15297973 15297974 A, G NOTCH3 chr19 15298135 15298136 A, C NOTCH3 chr19 15300068 15300069 C, T NOTCH3 chr19 15302843 15302844 C, T NOTCH3 chr19 15303224 15303225 A, G NOTCH3 chr19 15311544 15311545 C, G NOTCH3 chr19 17937515 17937516 C, T JAK3 chr19 17940815 17940816 C, G JAK3 chr19 17940841 17940842 A, G JAK3 chr19 17946803 17946804 A, G JAK3 chr19 17948731 17948732 C, T JAK3 chr19 17951018 17951019 C, T JAK3 chr19 17952184 17952185 G, T JAK3 chr19 17952404 17952405 C, T JAK3 chr19 17954214 17954215 G, T JAK3 chr19 17954596 17954597 C, G JAK3 chr19 17983502 17983503 G, T SLC5A5 chr19 17985290 17985291 A, C SLC5A5 chr19 17988793 17988794 C, T SLC5A5 chr19 17994572 17994573 A, C SLC5A5 chr19 17994593 17994594 A, G SLC5A5 chr19 17994604 17994605 A, C SLC5A5 chr19 17994634 17994635 C, T SLC5A5 chr19 17994643 17994644 C, T SLC5A5 chr19 17994835 17994836 A, G SLC5A5 chr19 18001838 18001839 A, G SLC5A5 chr19 18266698 18266699 C, T PIK3R2 chr19 18271763 18271764 C, T PIK3R2 chr19 18272189 18272190 A, C PIK3R2 chr19 18278127 18278128 C, T PIK3R2 chr19 18279637 18279638 C, T PIK3R2 chr19 18279996 18279997 C, T PIK3R2 chr19 18684562 18684563 C, T UBA52 chr19 18685822 18685823 A, G UBA52 chr19 18685963 18685964 G, T UBA52 chr19 30312873 30312874 C, T CCNE1 chr19 30313343 30313344 C, T CCNE1 chr19 30314537 30314538 G, T CCNE1 chr19 35823434 35823435 G, T CD22 chr19 35823603 35823604 A, G CD22 chr19 35828772 35828773 C, T CD22 chr19 35828902 35828903 A, G CD22 chr19 35829255 35829256 A, G CD22 chr19 35829380 35829381 A, G CD22 chr19 35831985 35831986 C, T CD22 chr19 35832388 35832389 A, G CD22 chr19 35832822 35832823 A, G CD22 chr19 35835939 35835940 C, T CD22 chr19 35836529 35836530 A, G CD22 chr19 35836599 35836600 A, C CD22 chr19 35837095 35837096 C, T CD22 chr19 35837149 35837150 C, T CD22 chr19 39787142 39787143 A, G IL29 chr19 39789114 39789115 A, G IL29 chr19 40739512 40739513 A, G AKT2 chr19 40739720 40739721 G, T AKT2 chr19 40747819 40747820 C, G AKT2 chr19 40748638 40748639 C, T AKT2 chr19 41725270 41725271 A, G AXL chr19 41725409 41725410 A, G AXL chr19 41737016 41737017 A, G AXL chr19 41745008 41745009 A, G AXL chr19 41748752 41748753 C, T AXL chr19 41758879 41758880 C, G AXL chr19 41759473 41759474 C, T AXL chr19 41765574 41765575 C, T AXL chr19 41765616 41765617 C, T AXL chr19 41854384 41854385 A, C TGFB1 chr19 41858589 41858590 C, T TGFB1 chr19 42212796 42212797 A, G CEACAM5 chr19 42213669 42213670 A, G CEACAM5 chr19 42213743 42213744 C, T CEACAM5 chr19 42213771 42213772 A, G CEACAM5 chr19 42213781 42213782 C, T CEACAM5 chr19 42213832 42213833 C, T CEACAM5 chr19 42213840 42213841 C, T CEACAM5 chr19 42213867 42213868 A, G CEACAM5 chr19 42213871 42213872 C, T CEACAM5 chr19 42213943 42213944 A, C CEACAM5 chr19 42221354 42221355 C, T CEACAM5 chr19 42221417 42221418 A, G CEACAM5 chr19 42221433 42221434 A, C CEACAM5 chr19 42221606 42221607 A, G CEACAM5 chr19 42222258 42222259 A, G CEACAM5 chr19 42222340 42222341 C, T CEACAM5 chr19 42224907 42224908 C, T CEACAM5 chr19 42224909 42224910 C, T CEACAM5 chr19 42224938 42224939 A, G CEACAM5 chr19 42225059 42225060 A, C CEACAM5 chr19 42470841 42470842 A, G ATP1A3 chr19 42470982 42470983 A, G ATP1A3 chr19 42471049 42471050 C, G ATP1A3 chr19 42474638 42474639 A, G ATP1A3 chr19 42489434 42489435 A, T ATP1A3 chr19 42489515 42489516 A, C ATP1A3 chr19 42492237 42492238 A, T ATP1A3 chr19 42492549 42492550 A, G ATP1A3 chr19 42791461 42791462 C, T CIC chr19 42793944 42793945 C, T CIC chr19 42795553 42795554 C, T CIC chr19 42796697 42796698 G, T CIC chr19 42798899 42798900 C, T CIC chr19 42798917 42798918 C, T CIC chr19 42798959 42798960 A, G CIC chr19 42799048 42799049 C, T CIC chr19 44047696 44047697 A, G XRCC1 chr19 44050194 44050195 C, T XRCC1 chr19 44050965 44050966 C, T XRCC1 chr19 44050980 44050981 A, G XRCC1 chr19 44055725 44055726 C, T XRCC1 chr19 44056340 44056341 C, T XRCC1 chr19 44056411 44056412 C, T XRCC1 chr19 44057718 44057719 G XRCC1 chr19 44065101 44065102 A, G XRCC1 chr19 45854918 45854919 G, T ERCC2 chr19 45855454 45855455 C, T ERCC2 chr19 45855523 45855524 A, G ERCC2 chr19 45856467 45856468 C, G ERCC2 chr19 45862193 45862194 A, G ERCC2 chr19 45867258 45867259 C, T ERCC2 chr19 45867675 45867676 A, C ERCC2 chr19 45868290 45868291 G, T ERCC2 chr19 45868308 45868309 G, T ERCC2 chr19 45871963 45871964 C, T ERCC2 chr19 47104778 47104779 A, C CALM3 chr19 47109150 47109151 C, G CALM3 chr19 47111644 47111645 A, G CALM3 chr19 47111662 47111663 C, T CALM3 chr19 47112206 47112207 C, T CALM3 chr19 47735874 47735875 C, T BBC3 chr19 49838890 49838891 A, C CD37 chr19 49838953 49838954 A, G CD37 chr19 49839014 49839015 C, T CD37 chr19 49839032 49839033 C, G CD37 chr19 49841202 49841203 A, G CD37 chr19 49842609 49842610 A, G CD37 chr19 49977928 49977929 A, G FLT3LG chr19 49978014 49978015 A, G FLT3LG chr19 49979397 49979398 A, G FLT3LG chr19 49983672 49983673 C, T FLT3LG chr19 50902163 50902164 A, G POLD1 chr19 50902330 50902331 C, T POLD1 chr19 50902658 50902659 C, G POLD1 chr19 50905073 50905074 A, G POLD1 chr19 50905188 50905189 G, T POLD1 chr19 50905189 50905190 C, T POLD1 chr19 50905309 50905310 A, G POLD1 chr19 50905411 50905412 A, G POLD1 chr19 50905654 50905655 A, G POLD1 chr19 50905761 50905762 C, T POLD1 chr19 50905876 50905877 G, T POLD1 chr19 50906274 50906275 C, T POLD1 chr19 50906297 50906298 C, T POLD1 chr19 50906784 50906785 C, T POLD1 chr19 50909628 50909629 A, G POLD1 chr19 50909764 50909765 C, T POLD1 chr19 50910283 50910284 A, G POLD1 chr19 50910292 50910293 C, T POLD1 chr19 50910533 50910534 C, T POLD1 chr19 50910537 50910538 C, T POLD1 chr19 50910609 50910610 C, T POLD1 chr19 50912125 50912126 A, G POLD1 chr19 50912417 50912418 C, G POLD1 chr19 50916771 50916772 C, T POLD1 chr19 50916810 50916811 A, G POLD1 chr19 50916975 50916976 A, G POLD1 chr19 50918757 50918758 C, T POLD1 chr19 50918968 50918969 A, G POLD1 chr19 50919796 50919797 C, T POLD1 chr19 50919827 50919828 A, G POLD1 chr19 50919837 50919838 C, T POLD1 chr19 50920409 50920410 C, T POLD1 chr19 50920534 50920535 C, T POLD1 chr19 50920535 50920536 A, G POLD1 chr19 51359542 51359543 A, G KLK3 chr19 51359565 51359566 A, G KLK3 chr19 51359715 51359716 A, G KLK3 chr19 51361381 51361382 A, G KLK3 chr19 51361471 51361472 A, C KLK3 chr19 51361756 51361757 C, T KLK3 chr19 51362803 51362804 A, G KLK3 chr19 51363397 51363398 C, T KLK3 chr19 51376836 51376837 C, G KLK2 chr19 51379892 51379893 C, T KLK2 chr19 51380109 51380110 A, T KLK2 chr19 51381776 51381777 C, T KLK2 chr19 51381792 51381793 A, C KLK2 chr19 52693456 52693457 A, C PPP2R1A chr19 52693508 52693509 G, T PPP2R1A chr19 52705298 52705299 A, G PPP2R1A chr19 52714578 52714579 A, C PPP2R1A chr19 52714718 52714719 C, T PPP2R1A chr19 52716142 52716143 A, G PPP2R1A chr19 52716411 52716412 C, T PPP2R1A chr19 52719189 52719190 A, G PPP2R1A chr19 52719961 52719962 C, T PPP2R1A chr19 52723366 52723367 A, G PPP2R1A chr19 52723435 52723436 C, T PPP2R1A chr19 52724215 52724216 C, G PPP2R1A chr19 52729029 52729030 C, T PPP2R1A chr19 52729081 52729082 A, C PPP2R1A chr19 55281314 55281315 G, T KIR2DL1 chr19 55286843 55286844 A, G KIR2DL1 chr19 55286863 55286864 A, C KIR2DL1 chr19 55294361 55294362 A, C KIR2DL1 chr19 55294926 55294927 A, G KIR2DL1 chr19 55295021 55295022 C, G KIR2DL1 chr19 55295035 55295036 C, G KIR2DL1 chr19 57742488 57742489 C, T AURKC chr19 57744008 57744009 A, G AURKC chr19 57744818 57744819 C, T AURKC chr19 57746287 57746288 A, G AURKC chr19 57746602 57746603 C, T AURKC chr20 3193841 3193842 A, C ITPA chr20 3193892 3193893 A, C ITPA chr20 3193977 3193978 A, G ITPA chr20 3195914 3195915 G, T ITPA chr20 3195940 3195941 A, G ITPA chr20 3203949 3203950 A, T ITPA chr20 3204083 3204084 A, G ITPA chr20 23016083 23016084 A, C SSTR4 chr20 23016147 23016148 G, T SSTR4 chr20 23016170 23016171 C, G SSTR4 chr20 23016969 23016970 G, T SSTR4 chr20 23017016 23017017 C, T SSTR4 chr20 23017043 23017044 C, T SSTR4 chr20 23017081 23017082 C, T SSTR4 chr20 30954294 30954295 A, G ASXL1 chr20 31017118 31017119 C, T ASXL1 chr20 31022468 31022469 A, G ASXL1 chr20 31022479 31022480 C, T ASXL1 chr20 31022764 31022765 C, T ASXL1 chr20 31022765 31022766 A, G ASXL1 chr20 31022909 31022910 G, T ASXL1 chr20 31023027 31023028 A, G ASXL1 chr20 31023499 31023500 C, T ASXL1 chr20 31024012 31024013 C, G ASXL1 chr20 31024033 31024034 A, G ASXL1 chr20 31024206 31024207 C, T ASXL1 chr20 31024273 31024274 C, T ASXL1 chr20 31024487 31024488 C, T ASXL1 chr20 31025162 31025163 A, G ASXL1 chr20 32264847 32264848 C E2F1 chr20 32264959 32264960 A, G E2F1 chr20 32273959 32273960 A, G E2F1 chr20 36022404 36022405 C, T SRC chr20 36024559 36024560 C, T SRC chr20 36030944 36030945 C, T SRC chr20 36760710 36760711 A, G TGM2 chr20 36767849 36767850 A, G TGM2 chr20 36769791 36769792 A, G TGM2 chr20 36770482 36770483 A, G TGM2 chr20 36770518 36770519 C, T TGM2 chr20 36770587 36770588 C, T TGM2 chr20 36775131 36775132 A, G TGM2 chr20 36775134 36775135 A, G TGM2 chr20 36775242 36775243 A, G TGM2 chr20 36776392 36776393 C, G TGM2 chr20 36793500 36793501 A, G TGM2 chr20 36793528 36793529 A, G TGM2 chr20 36793550 36793551 C, G TGM2 chr20 39657624 39657625 A, C TOP1 chr20 39728766 39728767 A, G TOP1 chr20 39743904 39743905 A, G TOP1 chr20 39743920 39743921 G, T TOP1 chr20 39788685 39788686 C, T PLCG1 chr20 39788815 39788816 A, G PLCG1 chr20 39791993 39791994 C, T PLCG1 chr20 39792001 39792002 C, T PLCG1 chr20 39792062 39792063 A, G PLCG1 chr20 39792537 39792538 C, T PLCG1 chr20 39793746 39793747 C, G PLCG1 chr20 39793846 39793847 A, C PLCG1 chr20 39794488 39794489 A, G PLCG1 chr20 39795462 39795463 C, T PLCG1 chr20 39797464 39797465 C, T PLCG1 chr20 39801011 39801012 C, T PLCG1 chr20 39802501 39802502 G, T PLCG1 chr20 39803077 39803078 C, T PLCG1 chr20 43252914 43252915 C, T ADA chr20 43254297 43254298 C, T ADA chr20 43254375 43254376 A, C ADA chr20 43255219 43255220 C, T ADA chr20 43264926 43264927 C, T ADA chr20 43264993 43264994 A, G ADA chr20 43280226 43280227 C, T ADA chr20 44746981 44746982 C, T CD40 chr20 44747085 44747086 A, G CD40 chr20 44747103 44747104 C, T CD40 chr20 44750423 44750424 C, T CD40 chr20 44751362 44751363 C, T CD40 chr20 44756822 44756823 C, T CD40 chr20 44756889 44756890 G, T CD40 chr20 44756890 44756891 A, G CD40 chr20 44756907 44756908 A, C CD40 chr20 44757017 44757018 C, T CD40 chr20 44757212 44757213 A, G CD40 chr20 44757288 44757289 G, T CD40 chr20 44757406 44757407 A, G CD40 chr20 44757523 44757524 C, G CD40 chr20 52188375 52188376 A, T ZNF217 chr20 52192307 52192308 A, C ZNF217 chr20 52192407 52192408 C, T ZNF217 chr20 52192452 52192453 A, G ZNF217 chr20 52192594 52192595 C, T ZNF217 chr20 52192636 52192637 C, T ZNF217 chr20 52192647 52192648 C, G ZNF217 chr20 52192689 52192690 G, T ZNF217 chr20 52192697 52192698 A, G ZNF217 chr20 52192788 52192789 C, T ZNF217 chr20 52193087 52193088 C, T ZNF217 chr20 52193213 52193214 A, G ZNF217 chr20 52193367 52193368 C, T ZNF217 chr20 52193659 52193660 A, G ZNF217 chr20 52193697 52193698 A, G ZNF217 chr20 52193721 52193722 A, G ZNF217 chr20 52198137 52198138 C, T ZNF217 chr20 52198339 52198340 A, T ZNF217 chr20 52198618 52198619 A, C ZNF217 chr20 52198966 52198967 A, G ZNF217 chr20 54959295 54959296 C, G AURKA chr20 54961540 54961541 A, T AURKA chr20 54963302 54963303 C, T AURKA chr20 54963319 54963320 C, T AURKA chr20 57415454 57415455 C, T GNAS chr20 57415875 57415876 A, C GNAS chr20 57428299 57428300 C, T GNAS chr20 57428819 57428820 A, G GNAS chr20 57428844 57428845 C, T GNAS chr20 57428946 57428947 A, G GNAS chr20 57429446 57429447 C, T GNAS chr20 57430556 57430557 A, T GNAS chr20 57430567 57430568 A, T GNAS chr20 57478680 57478681 C, T GNAS chr20 57478779 57478780 C, T GNAS chr20 57478797 57478798 A, G GNAS chr20 57478806 57478807 C, T GNAS chr20 57480366 57480367 G, T GNAS chr20 57480419 57480420 C, T GNAS chr20 57484240 57484241 C, T GNAS chr20 57484325 57484326 C, G GNAS chr20 57485116 57485117 C, T GNAS chr20 57485811 57485812 C, T GNAS chr20 62331932 62331933 A, G ARFRP1 chr20 62331988 62331989 G, T ARFRP1 chr20 62332024 62332025 C, T ARFRP1 chr20 62332536 62332537 C, T ARFRP1 chr20 62332640 62332641 C, T ARFRP1 chr20 62338144 62338145 A, G ARFRP1 chr21 36164343 36164344 A, C RUNX1 chr21 36164361 36164362 A, G RUNX1 chr21 36164485 36164486 C, G RUNX1 chr21 36171637 36171638 A, G RUNX1 chr21 36259307 36259308 C, T RUNX1 chr21 36262008 36262009 A, G RUNX1 chr21 37507500 37507501 A, G CBR3 chr21 37507739 37507740 C, G CBR3 chr21 37507768 37507769 C, T CBR3 chr21 37510223 37510224 C, T CBR3 chr21 37518581 37518582 A, G CBR3 chr21 37518678 37518679 A, T CBR3 chr21 37518705 37518706 A, G CBR3 chr21 37518797 37518798 A, G CBR3 chr21 37518812 37518813 A, G CBR3 chr21 37518849 37518850 A, G CBR3 chr21 39755606 39755607 A, G ERG chr21 39762882 39762883 C, T ERG chr21 39763535 39763536 C, G ERG chr21 39764210 39764211 A, T ERG chr21 39764260 39764261 C, G ERG chr21 39870309 39870310 A, G ERG chr21 39947521 39947522 C, T ERG chr21 39947696 39947697 A, G ERG chr21 42838103 42838104 C, G TMPRSS2 chr21 42842542 42842543 C, T TMPRSS2 chr21 42845382 42845383 A, G TMPRSS2 chr21 42852496 42852497 C, T TMPRSS2 chr21 42860306 42860307 C, T TMPRSS2 chr21 42860484 42860485 C, G TMPRSS2 chr21 42860493 42860494 C, G TMPRSS2 chr21 42861544 42861545 A, G TMPRSS2 chr21 42866295 42866296 C, T TMPRSS2 chr21 42879908 42879909 A, C TMPRSS2 chr21 46308794 46308795 A, G ITGB2 chr21 46311812 46311813 A, G ITGB2 chr21 46313441 46313442 G, T ITGB2 chr21 46318939 46318940 A, G ITGB2 chr21 46319068 46319069 C, T ITGB2 chr21 46326814 46326815 C, T ITGB2 chr21 46330182 46330183 C, T ITGB2 chr21 46330301 46330302 C, T ITGB2 chr21 46330486 46330487 A, G ITGB2 chr21 46330608 46330609 T ITGB2 chr21 46330627 46330628 C, T ITGB2 chr21 46918385 46918386 C, T SLC19A1 chr21 46918573 46918574 C, T SLC19A1 chr21 46935941 46935942 A, G SLC19A1 chr21 46951555 46951556 A, G SLC19A1 chr21 46952093 46952094 C, T SLC19A1 chr21 46954446 46954447 C, T SLC19A1 chr21 46957793 46957794 C, T SLC19A1 chr22 21288415 21288416 A, G CRKL chr22 22127316 22127317 A, G MAPK1 chr22 22221679 22221680 C, T MAPK1 chr22 22890491 22890492 A, G PRAME chr22 22890751 22890752 A, G PRAME chr22 22890755 22890756 A, G PRAME chr22 22890791 22890792 C, T PRAME chr22 22890868 22890869 C, T PRAME chr22 22890932 22890933 G PRAME chr22 22892334 22892335 A, G PRAME chr22 22892489 22892490 C, T PRAME chr22 22893391 22893392 C, G PRAME chr22 22895351 22895352 A, G PRAME chr22 22895391 22895392 A, G PRAME chr22 22895402 22895403 C, T PRAME chr22 22899233 22899234 A, G PRAME chr22 22899323 22899324 G, T PRAME chr22 23523308 23523309 C, T BCR chr22 23523629 23523630 A, C BCR chr22 23523752 23523753 C BCR chr22 23523968 23523969 A, G BCR chr22 23524465 23524466 G, T BCR chr22 23540509 23540510 A, G BCR chr22 23540608 23540609 A, G BCR chr22 23541424 23541425 A BCR chr22 23541487 23541488 C, T BCR chr22 23595923 23595924 T BCR chr22 23595995 23595996 C BCR chr22 23627237 23627238 A, C BCR chr22 23627368 23627369 A, G BCR chr22 23631800 23631801 C, T BCR chr22 23631822 23631823 C, T BCR chr22 23632512 23632513 A, G BCR chr22 23632546 23632547 A, G BCR chr22 23632620 23632621 A, C, G BCR chr22 23632635 23632636 A, C BCR chr22 23632664 23632665 A, C BCR chr22 23657612 23657613 C, T BCR chr22 24129325 24129326 C, T SMARCB1 chr22 24135881 24135882 C, T SMARCB1 chr22 24143205 24143206 A, G SMARCB1 chr22 24143383 24143384 C, T SMARCB1 chr22 24167512 24167513 A, G SMARCB1 chr22 29130457 29130458 C, T CHEK2 chr22 29664407 29664408 A, G EWSR1 chr22 29664422 29664423 A, G EWSR1 chr22 29668198 29668199 C, T EWSR1 chr22 29678560 29678561 C, T EWSR1 chr22 29688218 29688219 A, C EWSR1 chr22 29688631 29688632 G, T EWSR1 chr22 29693989 29693990 A, G EWSR1 chr22 29694916 29694917 A, G EWSR1 chr22 29695870 29695871 C, T EWSR1 chr22 29695998 29695999 C, T EWSR1 chr22 29696017 29696018 C, T EWSR1 chr22 29696068 29696069 C, T EWSR1 chr22 30038151 30038152 A, C NF2 chr22 30054301 30054302 C, T NF2 chr22 31532959 31532960 C, T PLA2G3 chr22 31533795 31533796 C, G PLA2G3 chr22 31533842 31533843 A, G PLA2G3 chr22 31533951 31533952 A, G PLA2G3 chr22 31533966 31533967 A, G PLA2G3 chr22 31535871 31535872 C, G PLA2G3 chr22 31535994 31535995 C, G PLA2G3 chr22 31536132 31536133 A, C PLA2G3 chr22 37602601 37602602 C, T SSTR3 chr22 37602610 37602611 C, G SSTR3 chr22 37603020 37603021 A, G SSTR3 chr22 37603050 37603051 C, T SSTR3 chr22 37603389 37603390 C, T SSTR3 chr22 37603743 37603744 C, T SSTR3 chr22 37603744 37603745 A, G SSTR3 chr22 38071706 38071707 A, G LGALS1 chr22 38074433 38074434 A, G LGALS1 chr22 38369975 38369976 A, G SOX10 chr22 38379542 38379543 A, G SOX10 chr22 38508467 38508468 C, T PLA2G6 chr22 38512243 38512244 A, G PLA2G6 chr22 38512401 38512402 A, G PLA2G6 chr22 38522548 38522549 A, G PLA2G6 chr22 38525560 38525561 A, G PLA2G6 chr22 38528957 38528958 C, T PLA2G6 chr22 38539083 38539084 A, C PLA2G6 chr22 38543409 38543410 A, G PLA2G6 chr22 38543452 38543453 C, T PLA2G6 chr22 38544456 38544457 C, T PLA2G6 chr22 38544571 38544572 C, T PLA2G6 chr22 38564040 38564041 C, G PLA2G6 chr22 38565208 38565209 A, G PLA2G6 chr22 38565261 38565262 C, T PLA2G6 chr22 38565346 38565347 C, T PLA2G6 chr22 39621796 39621797 G, T PDGFB chr22 39621892 39621893 C, T PDGFB chr22 39629417 39629418 C, T PDGFB chr22 39631712 39631713 C, T PDGFB chr22 39631746 39631747 C, G PDGFB chr22 39631767 39631768 G, T PDGFB chr22 39636828 39636829 A, T PDGFB chr22 39639852 39639853 G, T PDGFB chr22 41513174 41513175 C, T EP300 chr22 41523525 41523526 C, T EP300 chr22 41537191 41537192 C, T EP300 chr22 41537233 41537234 G, T EP300 chr22 41543982 41543983 C, G EP300 chr22 41545883 41545884 A, G EP300 chr22 41548007 41548008 A, G EP300 chr22 41551038 41551039 A, T EP300 chr22 41553258 41553259 A, G EP300 chr22 41553336 41553337 C, T EP300 chr22 41558837 41558838 C, G EP300 chr22 41559962 41559963 C, T EP300 chr22 41564707 41564708 A, C EP300 chr22 41568552 41568553 A, G EP300 chr22 41572540 41572541 C, T EP300 chr22 41574086 41574087 C, T EP300 chr22 42522612 42522613 C, G CYP2D6 chr22 42523942 42523943 A, G CYP2D6 chr22 42524946 42524947 C, T CYP2D6 chr22 42525131 42525132 C, G CYP2D6 chr22 42525133 42525134 C, T CYP2D6 chr22 42525727 42525728 A, C CYP2D6 chr22 42525755 42525756 A, G CYP2D6 chr22 42525771 42525772 A, G CYP2D6 chr22 42525797 42525798 C, G CYP2D6 chr22 42525810 42525811 C, T CYP2D6 chr22 42525951 42525952 A, C CYP2D6 chr22 42526570 42526571 C, G CYP2D6 chr22 42526572 42526573 G, T CYP2D6 chr22 42526579 42526580 C, G CYP2D6 chr22 42526693 42526694 A, G CYP2D6 chr22 42526762 42526763 C, T CYP2D6 chr22 42540356 42540357 C, G CYP2D6 chr22 46611262 46611263 A, G PPARA chr22 46614273 46614274 C, G PPARA chr22 46615879 46615880 C, T PPARA chr22 46615904 46615905 C, T PPARA chr22 46628118 46628119 C, G PPARA

APPENDIX 2 chr1 36768200 rs1573020 chr1 159174683 rs2814778 chr1 204790977 rs2065160 chr2 7149155 rs896788 chr2 109513601 rs3827760 chr2 136616754 rs182549 chr3 168645035 rs1498444 chr4 38803255 rs4540055 chr4 159181963 rs2026721 chr5 33951693 rs16891982 chr7 4457003 rs917118 chr10 17064992 rs7897550 chr10 34755348 rs1978806 chr11 32424389 rs5030240 chr12 29369871 rs10843344 chr12 56603834 rs773658 chr13 20901724 rs1335873 chr13 22374700 rs1886510 chr13 34864240 rs2065982 chr14 36170607 rs10141763 chr14 101142890 rs730570 chr15 28365618 rs12913832 chr15 48426484 rs1426654 chr16 31079371 rs881929 chr16 90105333 rs3785181 chr17 75551667 rs2304925 chr18 75432386 rs1024116 chr19 42410331 rs2303798 chr20 38849642 rs1321333 chr21 16685598 rs722098 chr21 17710424 rs239031 chr21 25672460 rs2572307 chr22 26350103 rs5997008 chr22 47836412 rs2040411 

1. A method for genomic and/or genetic analysis of a human nucleic acid sample comprising the following steps: a) providing a group of human reference genomes; b) testing of the human nucleic acid sample for sex and/or ancestry; c) selecting one or more population-specific human reference genomes, PHREGs, from the group of human reference genomes on the basis on the results of the sex and/or ancestry test in step b); and d) aligning the human nucleic acid sample to the selected PHREGs.
 2. The method of claim 1, wherein the alignment is performed on a majority allele level, or on a non-rare alleles level.
 3. The method of claim 1, comprising the additional step: e) performing variant calling of the aligned human nucleic acid sample with respect to the selected PHREGs.
 4. The method of claim 3, wherein the variant calling is performed on a majority allele level, or on a non-rare alleles level.
 5. The method of claim 1, wherein the human reference genomes provided in step a) are published human reference genomes or are derived from published human reference genomes.
 6. The method of claim 1, wherein step a) comprises adjusting the human reference genomes to an encoding level, the encoding level comprising either unique nucleotide codes or ambiguous nucleotide codes.
 7. The method of claim 1, wherein the human reference genomes provided in step a) are PHREGs.
 8. The method of claim 1, wherein the sex test comprises one or more of the following: testing at least one position in a sex-specific gene on chromosome X and/or on chromosome Y; leveraging alignment differences of human genome samples on chromosome X and/or chromosome Y; cytogenetic tests; FISH analysis; CGH analysis.
 9. The method of claim 1, wherein the ancestry test is based on a machine learning algorithm used on a human nucleic acid sample, or on another classification scheme that leverages ancestry-specific variants.
 10. The method of claim 1, wherein the ancestry test comprises using the genotype of at least one genomic position and/or testing of SNP arrays or SNP chips and/or testing of markers from Sanger sequencing or mass spectroscopy.
 11. The method of claim 1, wherein the ancestry test comprises testing at least one gene selected from the group of genes consisting of ABL2, ATP1A3, CIC, CYP2C8, CYP2C9, EPHA3, EPHA7, ERBB3, ERG, ETV1, F2, FAS, HFE, IL11RA, IL2RA, ITGB6, KIF11, KIT, KLK3, LRP6, MDM4, NAT2, NTRK2, PDGFB, PIK3R1, PLA2G3, PLAU, PRKCB, RICTOR, SLC7A11, STAT3, T, TSC1, VCAM1, VDR, VEGFB, ACVRL1, AXL, CA9, CALCR, CASP9, ENG, EPHB1, ERBB4, ESR1, FGFR2, HPSE, HSP90AA1, ITK, MRE11A, PLK1, PTPRC, SERPINE1, SMC4, TERT, TLR3, WISP3, WT1, XRCC1, ANGPT2, ARID2, BARD1, CBR3, CDH2, CYP1B1, DDR2, DNMT3A, EPCAM, ERCC2, FANCG, FANCL, GSTP1, IRS2, ITGB1, JAK3, LHCGR, MSH6, NCF2, RNF43, SLC5A5, TMPRSS2, TNFRSF8, AKT1, CD248, CD4, ESR2, EZH2, IGF1R, ITGAV, ITGB2, KLHL6, MAP3K1, MET, MLL, MTHFR, NFKB1, NUP93, PARP8, RB1, RPE65, TSHR, ABL1, BLM, CYP19A1, DPP4, EPHA6, ERBB2, EWSR1, FOXP4, ITGAM, KDM5A, LPA, LTK, MLH1, PBRM1, PHLPP2, SF3B1, TNFRSF10A, ABCG2, ACPP, ADAM15, DPYD, EPHA5, EPHB6, FOLH1, KDR, MSH3, MST1R, NTRK1, ROCK2, SLC6A2, TET2, TGM2, TH, ABCB1, CD22, CD40, CD44, CDH20, CYP11B2, ERCC5, GPR124, IL7R, ITGB3, ITGB5, NCL, NOD2, NR4A1, PGR, PLCG1, PPP2R1A, PRAME, PTCH2, RET, SETD2, XPC, ASXL1, EPHB4, PLA2G6, SYK, TET1, EP300, FLT1, ITGA1, LOXL2, PDGFRB, PIK3CD, SSTR5, TEC, APC, ATR, CLU, CREBBP, CYP2D6, EML4, MMP2, PARP2, PDGFRA, TRPM8, CSF1R, DOT1L, FGFR3, FGFR4, GLP2R, IKBKE, JAK1, NOTCH2, SPEN, SPG7, BRCA1, CYP11B1, GNAS, ITGA5, LTF, NRP2, PTK2B, TNKS, ABCC1, CEACAM5, CYP4B1, EGFR, FLT3, INSR, PTCH1, SMARCA4, ZNF217, BCR, EEF2, SELP, SLCO1B1, ABCC2, FLT4, MTR, IL4R, MTOR, RPTOR, TEK, ATM, CARD11, FANCD2, MEFV, NF1, TP73, BRCA2, CD109, PTPRD, ABCC6, IGF2R, P2RX7, ROS1, ACE, PARP1, PRKDC, CENPE, TSC2, ALK, NOTCH1, TNC, NOTCH3, POLE, MLL2, MYH11, POLD1, GRIN3B, F5, FANCA, LRP1B, LRP2, VWF.
 12. The method of claim 1, wherein the human nucleic acid sample comprises a set of reads issued from a next-generation sequencing procedure, NGS, and wherein the alignment comprises a step of mapping the reads to the selected PHREGs.
 13. A computer system for genomic and/or genetic analysis of a human nucleic acid sample, the computer system comprising: a) a first module comprising computer instructions for providing a group of human reference genomes; b) a second module for testing of a human nucleic acid sample for sex and/or ancestry; c) a third module comprising computer instructions for selecting one or more population-specific human reference genomes, PHREGs, from the group of human reference genomes on the basis of the results of the sex and/or ancestry test; and d) a fourth module comprising computer instructions for aligning the human nucleic acid sample to the determined PHREGs.
 14. Computer program comprising instructions which, when the program is executed by a computer, cause the computer to carry out the steps a), b), c) and d) of the method of claim
 1. 15. Computer-readable storage medium comprising instructions which, when executed by a computer, cause the computer to carry out the steps a), b), c) and d) of the method of claim
 1. 16. A method of treating a patient comprising Retrieving an identification of a disease indication of the patient, Obtaining a nucleic acid sample from the patient Performing genomic and/or genetic analysis of the nucleic acid sample according to the method of claim 1, Retrieving possible treatments for the disease indication of the patient Performing variant calling and interpretation Classification of the retrieved possible treatments based on the variant interpretation, wherein a treatment is classified as indicated for the patient or contraindicated for the patient Selecting one of the indicated treatments Treating of the patient according to the selected treatment. 